module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x20mers.unique.bam OUTPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x20mers.unique.dedup.bam METRICS_FILE=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x20mers.unique.bam OUTPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x20mers.unique.dedup.bam METRICS_FILE=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x20mers.unique.bam OUTPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x20mers.unique.dedup.bam METRICS_FILE=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x20mers.unique.bam OUTPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x20mers.unique.dedup.bam METRICS_FILE=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x20mers.unique.bam OUTPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x20mers.unique.dedup.bam METRICS_FILE=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x20mers.unique.bam OUTPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x20mers.unique.dedup.bam METRICS_FILE=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x20mers.unique.bam OUTPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x20mers.unique.dedup.bam METRICS_FILE=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x20mers.unique.bam OUTPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x20mers.unique.dedup.bam METRICS_FILE=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x20mers.unique.bam OUTPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x20mers.unique.dedup.bam METRICS_FILE=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x20mers.unique.bam OUTPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x20mers.unique.dedup.bam METRICS_FILE=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x20mers.unique.bam OUTPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x20mers.unique.dedup.bam METRICS_FILE=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x20mers.unique.bam OUTPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x20mers.unique.dedup.bam METRICS_FILE=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x20mers.unique.bam OUTPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x20mers.unique.dedup.bam METRICS_FILE=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x20mers.unique.bam OUTPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x20mers.unique.dedup.bam METRICS_FILE=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x20mers.unique.bam OUTPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x20mers.unique.dedup.bam METRICS_FILE=L1062-Training_camp_33-WT-0min-rep2-srstern.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x20mers.unique.bam OUTPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x20mers.unique.dedup.bam METRICS_FILE=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x20mers.unique.bam OUTPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x20mers.unique.dedup.bam METRICS_FILE=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x20mers.unique.bam OUTPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x20mers.unique.dedup.bam METRICS_FILE=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L665-FUN30.2x20mers.unique.bam OUTPUT=L665-FUN30.2x20mers.unique.dedup.bam METRICS_FILE=L665-FUN30.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L666-MSS11.2x20mers.unique.bam OUTPUT=L666-MSS11.2x20mers.unique.dedup.bam METRICS_FILE=L666-MSS11.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L667-YAP7.2x20mers.unique.bam OUTPUT=L667-YAP7.2x20mers.unique.dedup.bam METRICS_FILE=L667-YAP7.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L668-CUP9.2x20mers.unique.bam OUTPUT=L668-CUP9.2x20mers.unique.dedup.bam METRICS_FILE=L668-CUP9.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L669-ARG80.2x20mers.unique.bam OUTPUT=L669-ARG80.2x20mers.unique.dedup.bam METRICS_FILE=L669-ARG80.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L670-ARP6.2x20mers.unique.bam OUTPUT=L670-ARP6.2x20mers.unique.dedup.bam METRICS_FILE=L670-ARP6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L671-HAP5.2x20mers.unique.bam OUTPUT=L671-HAP5.2x20mers.unique.dedup.bam METRICS_FILE=L671-HAP5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L672-CAT8.2x20mers.unique.bam OUTPUT=L672-CAT8.2x20mers.unique.dedup.bam METRICS_FILE=L672-CAT8.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L673-RDS2.2x20mers.unique.bam OUTPUT=L673-RDS2.2x20mers.unique.dedup.bam METRICS_FILE=L673-RDS2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L674-CIN5.2x20mers.unique.bam OUTPUT=L674-CIN5.2x20mers.unique.dedup.bam METRICS_FILE=L674-CIN5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L675-RDR1.2x20mers.unique.bam OUTPUT=L675-RDR1.2x20mers.unique.dedup.bam METRICS_FILE=L675-RDR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L676-AFT2.2x20mers.unique.bam OUTPUT=L676-AFT2.2x20mers.unique.dedup.bam METRICS_FILE=L676-AFT2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L677-YAP1.2x20mers.unique.bam OUTPUT=L677-YAP1.2x20mers.unique.dedup.bam METRICS_FILE=L677-YAP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L678-IOC2.2x20mers.unique.bam OUTPUT=L678-IOC2.2x20mers.unique.dedup.bam METRICS_FILE=L678-IOC2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L679-MAC1.2x20mers.unique.bam OUTPUT=L679-MAC1.2x20mers.unique.dedup.bam METRICS_FILE=L679-MAC1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L680-RTG1.2x20mers.unique.bam OUTPUT=L680-RTG1.2x20mers.unique.dedup.bam METRICS_FILE=L680-RTG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L681-RGM1.2x20mers.unique.bam OUTPUT=L681-RGM1.2x20mers.unique.dedup.bam METRICS_FILE=L681-RGM1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L682-ERT1.2x20mers.unique.bam OUTPUT=L682-ERT1.2x20mers.unique.dedup.bam METRICS_FILE=L682-ERT1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L683-TYE7.2x20mers.unique.bam OUTPUT=L683-TYE7.2x20mers.unique.dedup.bam METRICS_FILE=L683-TYE7.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L684-DAL82.2x20mers.unique.bam OUTPUT=L684-DAL82.2x20mers.unique.dedup.bam METRICS_FILE=L684-DAL82.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L685-TEA1.2x20mers.unique.bam OUTPUT=L685-TEA1.2x20mers.unique.dedup.bam METRICS_FILE=L685-TEA1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L686-USV1.2x20mers.unique.bam OUTPUT=L686-USV1.2x20mers.unique.dedup.bam METRICS_FILE=L686-USV1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L687-SMP1.2x20mers.unique.bam OUTPUT=L687-SMP1.2x20mers.unique.dedup.bam METRICS_FILE=L687-SMP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L688-ABF2.2x20mers.unique.bam OUTPUT=L688-ABF2.2x20mers.unique.dedup.bam METRICS_FILE=L688-ABF2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L689-MBP1.2x20mers.unique.bam OUTPUT=L689-MBP1.2x20mers.unique.dedup.bam METRICS_FILE=L689-MBP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L690-CRZ1.2x20mers.unique.bam OUTPUT=L690-CRZ1.2x20mers.unique.dedup.bam METRICS_FILE=L690-CRZ1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L691-FKH2.2x20mers.unique.bam OUTPUT=L691-FKH2.2x20mers.unique.dedup.bam METRICS_FILE=L691-FKH2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L692-GAT4.2x20mers.unique.bam OUTPUT=L692-GAT4.2x20mers.unique.dedup.bam METRICS_FILE=L692-GAT4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L693-STP4.2x20mers.unique.bam OUTPUT=L693-STP4.2x20mers.unique.dedup.bam METRICS_FILE=L693-STP4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L694-IOC3.2x20mers.unique.bam OUTPUT=L694-IOC3.2x20mers.unique.dedup.bam METRICS_FILE=L694-IOC3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L695-NRG2.2x20mers.unique.bam OUTPUT=L695-NRG2.2x20mers.unique.dedup.bam METRICS_FILE=L695-NRG2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L697-CST9.2x20mers.unique.bam OUTPUT=L697-CST9.2x20mers.unique.dedup.bam METRICS_FILE=L697-CST9.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L698-CST6.2x20mers.unique.bam OUTPUT=L698-CST6.2x20mers.unique.dedup.bam METRICS_FILE=L698-CST6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L699-WAR1.2x20mers.unique.bam OUTPUT=L699-WAR1.2x20mers.unique.dedup.bam METRICS_FILE=L699-WAR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L701-DAL80.2x20mers.unique.bam OUTPUT=L701-DAL80.2x20mers.unique.dedup.bam METRICS_FILE=L701-DAL80.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L702-SIR2.2x20mers.unique.bam OUTPUT=L702-SIR2.2x20mers.unique.dedup.bam METRICS_FILE=L702-SIR2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L704-REC8.2x20mers.unique.bam OUTPUT=L704-REC8.2x20mers.unique.dedup.bam METRICS_FILE=L704-REC8.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L705-TBS1.2x20mers.unique.bam OUTPUT=L705-TBS1.2x20mers.unique.dedup.bam METRICS_FILE=L705-TBS1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L706-URC2.2x20mers.unique.bam OUTPUT=L706-URC2.2x20mers.unique.dedup.bam METRICS_FILE=L706-URC2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L708-HDA1.2x20mers.unique.bam OUTPUT=L708-HDA1.2x20mers.unique.dedup.bam METRICS_FILE=L708-HDA1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L710-ASG1.2x20mers.unique.bam OUTPUT=L710-ASG1.2x20mers.unique.dedup.bam METRICS_FILE=L710-ASG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L713-YNR063W.2x20mers.unique.bam OUTPUT=L713-YNR063W.2x20mers.unique.dedup.bam METRICS_FILE=L713-YNR063W.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L716-HOG1.2x20mers.unique.bam OUTPUT=L716-HOG1.2x20mers.unique.dedup.bam METRICS_FILE=L716-HOG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L717-DOT6.2x20mers.unique.bam OUTPUT=L717-DOT6.2x20mers.unique.dedup.bam METRICS_FILE=L717-DOT6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L718-MSN1.2x20mers.unique.bam OUTPUT=L718-MSN1.2x20mers.unique.dedup.bam METRICS_FILE=L718-MSN1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L720-INO4.2x20mers.unique.bam OUTPUT=L720-INO4.2x20mers.unique.dedup.bam METRICS_FILE=L720-INO4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L721-BYE1.2x20mers.unique.bam OUTPUT=L721-BYE1.2x20mers.unique.dedup.bam METRICS_FILE=L721-BYE1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L722-LSM1.2x20mers.unique.bam OUTPUT=L722-LSM1.2x20mers.unique.dedup.bam METRICS_FILE=L722-LSM1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L723-YER064C.2x20mers.unique.bam OUTPUT=L723-YER064C.2x20mers.unique.dedup.bam METRICS_FILE=L723-YER064C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L725-YFL052W.2x20mers.unique.bam OUTPUT=L725-YFL052W.2x20mers.unique.dedup.bam METRICS_FILE=L725-YFL052W.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L726-HAL9.2x20mers.unique.bam OUTPUT=L726-HAL9.2x20mers.unique.dedup.bam METRICS_FILE=L726-HAL9.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L727-RPH1.2x20mers.unique.bam OUTPUT=L727-RPH1.2x20mers.unique.dedup.bam METRICS_FILE=L727-RPH1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L730-GAT1.2x20mers.unique.bam OUTPUT=L730-GAT1.2x20mers.unique.dedup.bam METRICS_FILE=L730-GAT1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L732-YER130C.2x20mers.unique.bam OUTPUT=L732-YER130C.2x20mers.unique.dedup.bam METRICS_FILE=L732-YER130C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L733-RTG3.2x20mers.unique.bam OUTPUT=L733-RTG3.2x20mers.unique.dedup.bam METRICS_FILE=L733-RTG3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L734-SWI4.2x20mers.unique.bam OUTPUT=L734-SWI4.2x20mers.unique.dedup.bam METRICS_FILE=L734-SWI4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L735-RPN4.2x20mers.unique.bam OUTPUT=L735-RPN4.2x20mers.unique.dedup.bam METRICS_FILE=L735-RPN4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L736-SPO11.2x20mers.unique.bam OUTPUT=L736-SPO11.2x20mers.unique.dedup.bam METRICS_FILE=L736-SPO11.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L737-STB5.2x20mers.unique.bam OUTPUT=L737-STB5.2x20mers.unique.dedup.bam METRICS_FILE=L737-STB5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L738-NDT80.2x20mers.unique.bam OUTPUT=L738-NDT80.2x20mers.unique.dedup.bam METRICS_FILE=L738-NDT80.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L739-GIS1.2x20mers.unique.bam OUTPUT=L739-GIS1.2x20mers.unique.dedup.bam METRICS_FILE=L739-GIS1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L740-LEU3.2x20mers.unique.bam OUTPUT=L740-LEU3.2x20mers.unique.dedup.bam METRICS_FILE=L740-LEU3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L741-YAP3.2x20mers.unique.bam OUTPUT=L741-YAP3.2x20mers.unique.dedup.bam METRICS_FILE=L741-YAP3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L742-NRG1.2x20mers.unique.bam OUTPUT=L742-NRG1.2x20mers.unique.dedup.bam METRICS_FILE=L742-NRG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L743-MSN4.2x20mers.unique.bam OUTPUT=L743-MSN4.2x20mers.unique.dedup.bam METRICS_FILE=L743-MSN4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L744-ASH1.2x20mers.unique.bam OUTPUT=L744-ASH1.2x20mers.unique.dedup.bam METRICS_FILE=L744-ASH1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L745-HAP4.2x20mers.unique.bam OUTPUT=L745-HAP4.2x20mers.unique.dedup.bam METRICS_FILE=L745-HAP4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L746-HPC2.2x20mers.unique.bam OUTPUT=L746-HPC2.2x20mers.unique.dedup.bam METRICS_FILE=L746-HPC2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L747-TOS8.2x20mers.unique.bam OUTPUT=L747-TOS8.2x20mers.unique.dedup.bam METRICS_FILE=L747-TOS8.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L748-HOT1.2x20mers.unique.bam OUTPUT=L748-HOT1.2x20mers.unique.dedup.bam METRICS_FILE=L748-HOT1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L749-KAR4.2x20mers.unique.bam OUTPUT=L749-KAR4.2x20mers.unique.dedup.bam METRICS_FILE=L749-KAR4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L750-AZF1.2x20mers.unique.bam OUTPUT=L750-AZF1.2x20mers.unique.dedup.bam METRICS_FILE=L750-AZF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L751-ELG1.2x20mers.unique.bam OUTPUT=L751-ELG1.2x20mers.unique.dedup.bam METRICS_FILE=L751-ELG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L752-YGR067C.2x20mers.unique.bam OUTPUT=L752-YGR067C.2x20mers.unique.dedup.bam METRICS_FILE=L752-YGR067C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L753-unknown.2x20mers.unique.bam OUTPUT=L753-unknown.2x20mers.unique.dedup.bam METRICS_FILE=L753-unknown.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L754-LYS14.2x20mers.unique.bam OUTPUT=L754-LYS14.2x20mers.unique.dedup.bam METRICS_FILE=L754-LYS14.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L755-HIR3.2x20mers.unique.bam OUTPUT=L755-HIR3.2x20mers.unique.dedup.bam METRICS_FILE=L755-HIR3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L756-STB4.2x20mers.unique.bam OUTPUT=L756-STB4.2x20mers.unique.dedup.bam METRICS_FILE=L756-STB4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L757-KTI12.2x20mers.unique.bam OUTPUT=L757-KTI12.2x20mers.unique.dedup.bam METRICS_FILE=L757-KTI12.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L758-SKN7.2x20mers.unique.bam OUTPUT=L758-SKN7.2x20mers.unique.dedup.bam METRICS_FILE=L758-SKN7.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L759-RME1.2x20mers.unique.bam OUTPUT=L759-RME1.2x20mers.unique.dedup.bam METRICS_FILE=L759-RME1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L760-ISW1.2x20mers.unique.bam OUTPUT=L760-ISW1.2x20mers.unique.dedup.bam METRICS_FILE=L760-ISW1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L761-FZF1.2x20mers.unique.bam OUTPUT=L761-FZF1.2x20mers.unique.dedup.bam METRICS_FILE=L761-FZF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L762-SIP4.2x20mers.unique.bam OUTPUT=L762-SIP4.2x20mers.unique.dedup.bam METRICS_FILE=L762-SIP4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L763-PUT3.2x20mers.unique.bam OUTPUT=L763-PUT3.2x20mers.unique.dedup.bam METRICS_FILE=L763-PUT3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L764-STP2.2x20mers.unique.bam OUTPUT=L764-STP2.2x20mers.unique.dedup.bam METRICS_FILE=L764-STP2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L765-GZF3.2x20mers.unique.bam OUTPUT=L765-GZF3.2x20mers.unique.dedup.bam METRICS_FILE=L765-GZF3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L766-BAS1.2x20mers.unique.bam OUTPUT=L766-BAS1.2x20mers.unique.dedup.bam METRICS_FILE=L766-BAS1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L767-SUT2.2x20mers.unique.bam OUTPUT=L767-SUT2.2x20mers.unique.dedup.bam METRICS_FILE=L767-SUT2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L768-ROX1.2x20mers.unique.bam OUTPUT=L768-ROX1.2x20mers.unique.dedup.bam METRICS_FILE=L768-ROX1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L769-LIF1.2x20mers.unique.bam OUTPUT=L769-LIF1.2x20mers.unique.dedup.bam METRICS_FILE=L769-LIF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L770-THO1.2x20mers.unique.bam OUTPUT=L770-THO1.2x20mers.unique.dedup.bam METRICS_FILE=L770-THO1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L771-HDA2.2x20mers.unique.bam OUTPUT=L771-HDA2.2x20mers.unique.dedup.bam METRICS_FILE=L771-HDA2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L772-NUP170.2x20mers.unique.bam OUTPUT=L772-NUP170.2x20mers.unique.dedup.bam METRICS_FILE=L772-NUP170.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L773-YPR015C.2x20mers.unique.bam OUTPUT=L773-YPR015C.2x20mers.unique.dedup.bam METRICS_FILE=L773-YPR015C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L774-SUB1.2x20mers.unique.bam OUTPUT=L774-SUB1.2x20mers.unique.dedup.bam METRICS_FILE=L774-SUB1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L775-IME1.2x20mers.unique.bam OUTPUT=L775-IME1.2x20mers.unique.dedup.bam METRICS_FILE=L775-IME1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L776-HIR1.2x20mers.unique.bam OUTPUT=L776-HIR1.2x20mers.unique.dedup.bam METRICS_FILE=L776-HIR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L777-MET32.2x20mers.unique.bam OUTPUT=L777-MET32.2x20mers.unique.dedup.bam METRICS_FILE=L777-MET32.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L778-RLM1.2x20mers.unique.bam OUTPUT=L778-RLM1.2x20mers.unique.dedup.bam METRICS_FILE=L778-RLM1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L779-YTA7.2x20mers.unique.bam OUTPUT=L779-YTA7.2x20mers.unique.dedup.bam METRICS_FILE=L779-YTA7.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L780-HIR2.2x20mers.unique.bam OUTPUT=L780-HIR2.2x20mers.unique.dedup.bam METRICS_FILE=L780-HIR2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L781-ZAP1.2x20mers.unique.bam OUTPUT=L781-ZAP1.2x20mers.unique.dedup.bam METRICS_FILE=L781-ZAP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L782-RDS1.2x20mers.unique.bam OUTPUT=L782-RDS1.2x20mers.unique.dedup.bam METRICS_FILE=L782-RDS1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L783-BDF1.2x20mers.unique.bam OUTPUT=L783-BDF1.2x20mers.unique.dedup.bam METRICS_FILE=L783-BDF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L784-HDA3.2x20mers.unique.bam OUTPUT=L784-HDA3.2x20mers.unique.dedup.bam METRICS_FILE=L784-HDA3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L785-CAD1.2x20mers.unique.bam OUTPUT=L785-CAD1.2x20mers.unique.dedup.bam METRICS_FILE=L785-CAD1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L786-SIR4.2x20mers.unique.bam OUTPUT=L786-SIR4.2x20mers.unique.dedup.bam METRICS_FILE=L786-SIR4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L787-REF2.2x20mers.unique.bam OUTPUT=L787-REF2.2x20mers.unique.dedup.bam METRICS_FILE=L787-REF2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L788-MET31.2x20mers.unique.bam OUTPUT=L788-MET31.2x20mers.unique.dedup.bam METRICS_FILE=L788-MET31.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L789-ARO80.2x20mers.unique.bam OUTPUT=L789-ARO80.2x20mers.unique.dedup.bam METRICS_FILE=L789-ARO80.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L790-RSF2.2x20mers.unique.bam OUTPUT=L790-RSF2.2x20mers.unique.dedup.bam METRICS_FILE=L790-RSF2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L791-CTF4.2x20mers.unique.bam OUTPUT=L791-CTF4.2x20mers.unique.dedup.bam METRICS_FILE=L791-CTF4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L792-CDC73.2x20mers.unique.bam OUTPUT=L792-CDC73.2x20mers.unique.dedup.bam METRICS_FILE=L792-CDC73.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L793-OAF1.2x20mers.unique.bam OUTPUT=L793-OAF1.2x20mers.unique.dedup.bam METRICS_FILE=L793-OAF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L794-UPC2.2x20mers.unique.bam OUTPUT=L794-UPC2.2x20mers.unique.dedup.bam METRICS_FILE=L794-UPC2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L795-MIG3.2x20mers.unique.bam OUTPUT=L795-MIG3.2x20mers.unique.dedup.bam METRICS_FILE=L795-MIG3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L796-UME6.2x20mers.unique.bam OUTPUT=L796-UME6.2x20mers.unique.dedup.bam METRICS_FILE=L796-UME6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L797-REI1.2x20mers.unique.bam OUTPUT=L797-REI1.2x20mers.unique.dedup.bam METRICS_FILE=L797-REI1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L798-YLR278C.2x20mers.unique.bam OUTPUT=L798-YLR278C.2x20mers.unique.dedup.bam METRICS_FILE=L798-YLR278C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L799-SFP1.2x20mers.unique.bam OUTPUT=L799-SFP1.2x20mers.unique.dedup.bam METRICS_FILE=L799-SFP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L800-ECM23.2x20mers.unique.bam OUTPUT=L800-ECM23.2x20mers.unique.dedup.bam METRICS_FILE=L800-ECM23.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L801-VHR1.2x20mers.unique.bam OUTPUT=L801-VHR1.2x20mers.unique.dedup.bam METRICS_FILE=L801-VHR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L802-DHH1.2x20mers.unique.bam OUTPUT=L802-DHH1.2x20mers.unique.dedup.bam METRICS_FILE=L802-DHH1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L803-YAP6.2x20mers.unique.bam OUTPUT=L803-YAP6.2x20mers.unique.dedup.bam METRICS_FILE=L803-YAP6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L804-GCN4.2x20mers.unique.bam OUTPUT=L804-GCN4.2x20mers.unique.dedup.bam METRICS_FILE=L804-GCN4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L805-PDR1.2x20mers.unique.bam OUTPUT=L805-PDR1.2x20mers.unique.dedup.bam METRICS_FILE=L805-PDR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L806-MIG2.2x20mers.unique.bam OUTPUT=L806-MIG2.2x20mers.unique.dedup.bam METRICS_FILE=L806-MIG2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L807-ADR1.2x20mers.unique.bam OUTPUT=L807-ADR1.2x20mers.unique.dedup.bam METRICS_FILE=L807-ADR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L808-YPR022C.2x20mers.unique.bam OUTPUT=L808-YPR022C.2x20mers.unique.dedup.bam METRICS_FILE=L808-YPR022C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L809-HAA1.2x20mers.unique.bam OUTPUT=L809-HAA1.2x20mers.unique.dedup.bam METRICS_FILE=L809-HAA1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L810-ARR1.2x20mers.unique.bam OUTPUT=L810-ARR1.2x20mers.unique.dedup.bam METRICS_FILE=L810-ARR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L811-YPR013C.2x20mers.unique.bam OUTPUT=L811-YPR013C.2x20mers.unique.dedup.bam METRICS_FILE=L811-YPR013C.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L812-RGT1.2x20mers.unique.bam OUTPUT=L812-RGT1.2x20mers.unique.dedup.bam METRICS_FILE=L812-RGT1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L813-RFX1.2x20mers.unique.bam OUTPUT=L813-RFX1.2x20mers.unique.dedup.bam METRICS_FILE=L813-RFX1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L814-IXR1.2x20mers.unique.bam OUTPUT=L814-IXR1.2x20mers.unique.dedup.bam METRICS_FILE=L814-IXR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L815-PDR8.2x20mers.unique.bam OUTPUT=L815-PDR8.2x20mers.unique.dedup.bam METRICS_FILE=L815-PDR8.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L816-ECM22.2x20mers.unique.bam OUTPUT=L816-ECM22.2x20mers.unique.dedup.bam METRICS_FILE=L816-ECM22.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L817-XRN1.2x20mers.unique.bam OUTPUT=L817-XRN1.2x20mers.unique.dedup.bam METRICS_FILE=L817-XRN1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L818-YRR1.2x20mers.unique.bam OUTPUT=L818-YRR1.2x20mers.unique.dedup.bam METRICS_FILE=L818-YRR1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L819-MSN2.2x20mers.unique.bam OUTPUT=L819-MSN2.2x20mers.unique.dedup.bam METRICS_FILE=L819-MSN2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L820-YPR196W.2x20mers.unique.bam OUTPUT=L820-YPR196W.2x20mers.unique.dedup.bam METRICS_FILE=L820-YPR196W.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L821-DAL81.2x20mers.unique.bam OUTPUT=L821-DAL81.2x20mers.unique.dedup.bam METRICS_FILE=L821-DAL81.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L822-HAT1.2x20mers.unique.bam OUTPUT=L822-HAT1.2x20mers.unique.dedup.bam METRICS_FILE=L822-HAT1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L823-PAF1.2x20mers.unique.bam OUTPUT=L823-PAF1.2x20mers.unique.dedup.bam METRICS_FILE=L823-PAF1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L824-NHP10.2x20mers.unique.bam OUTPUT=L824-NHP10.2x20mers.unique.dedup.bam METRICS_FILE=L824-NHP10.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L825-SPP1.2x20mers.unique.bam OUTPUT=L825-SPP1.2x20mers.unique.dedup.bam METRICS_FILE=L825-SPP1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L826-SFL1.2x20mers.unique.bam OUTPUT=L826-SFL1.2x20mers.unique.dedup.bam METRICS_FILE=L826-SFL1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L827-STP3.2x20mers.unique.bam OUTPUT=L827-STP3.2x20mers.unique.dedup.bam METRICS_FILE=L827-STP3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L828-YRM1.2x20mers.unique.bam OUTPUT=L828-YRM1.2x20mers.unique.dedup.bam METRICS_FILE=L828-YRM1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L829-ISW2.2x20mers.unique.bam OUTPUT=L829-ISW2.2x20mers.unique.dedup.bam METRICS_FILE=L829-ISW2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L830-HTZ1.2x20mers.unique.bam OUTPUT=L830-HTZ1.2x20mers.unique.dedup.bam METRICS_FILE=L830-HTZ1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L831-PHD1.2x20mers.unique.bam OUTPUT=L831-PHD1.2x20mers.unique.dedup.bam METRICS_FILE=L831-PHD1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L832-SWI5.2x20mers.unique.bam OUTPUT=L832-SWI5.2x20mers.unique.dedup.bam METRICS_FILE=L832-SWI5.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L833-ACA1.2x20mers.unique.bam OUTPUT=L833-ACA1.2x20mers.unique.dedup.bam METRICS_FILE=L833-ACA1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L834-INO2.2x20mers.unique.bam OUTPUT=L834-INO2.2x20mers.unique.dedup.bam METRICS_FILE=L834-INO2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L835-PHO4.2x20mers.unique.bam OUTPUT=L835-PHO4.2x20mers.unique.dedup.bam METRICS_FILE=L835-PHO4.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L836-MGA1.2x20mers.unique.bam OUTPUT=L836-MGA1.2x20mers.unique.dedup.bam METRICS_FILE=L836-MGA1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L837-MIG1.2x20mers.unique.bam OUTPUT=L837-MIG1.2x20mers.unique.dedup.bam METRICS_FILE=L837-MIG1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L838-HAP3.2x20mers.unique.bam OUTPUT=L838-HAP3.2x20mers.unique.dedup.bam METRICS_FILE=L838-HAP3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L839-YHR177W.2x20mers.unique.bam OUTPUT=L839-YHR177W.2x20mers.unique.dedup.bam METRICS_FILE=L839-YHR177W.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L847-GLN3.2x20mers.unique.bam OUTPUT=L847-GLN3.2x20mers.unique.dedup.bam METRICS_FILE=L847-GLN3.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L848-TOD6.2x20mers.unique.bam OUTPUT=L848-TOD6.2x20mers.unique.dedup.bam METRICS_FILE=L848-TOD6.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L925-MSN2-0min-rep1.2x20mers.unique.bam OUTPUT=L925-MSN2-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L925-MSN2-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L927-MSN1-0min-rep1.2x20mers.unique.bam OUTPUT=L927-MSN1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L927-MSN1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L928-HOG1-0min-rep1.2x20mers.unique.bam OUTPUT=L928-HOG1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L928-HOG1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L929-BDF1-0min-rep1.2x20mers.unique.bam OUTPUT=L929-BDF1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L929-BDF1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L930-YAP7-0min-rep1.2x20mers.unique.bam OUTPUT=L930-YAP7-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L930-YAP7-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L931-UME6-0min-rep1.2x20mers.unique.bam OUTPUT=L931-UME6-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L931-UME6-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L932-SMP1-0min-rep1.2x20mers.unique.bam OUTPUT=L932-SMP1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L932-SMP1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L933-YAP1-0min-rep1.2x20mers.unique.bam OUTPUT=L933-YAP1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L933-YAP1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L934-YAP3-0min-rep1.2x20mers.unique.bam OUTPUT=L934-YAP3-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L934-YAP3-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L935-ARR1-0min-rep1.2x20mers.unique.bam OUTPUT=L935-ARR1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L935-ARR1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L936-PHO4-0min-rep1.2x20mers.unique.bam OUTPUT=L936-PHO4-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L936-PHO4-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L937-YAP6-0min-rep1.2x20mers.unique.bam OUTPUT=L937-YAP6-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L937-YAP6-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L938-PDR3-0min-rep1.2x20mers.unique.bam OUTPUT=L938-PDR3-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L938-PDR3-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L939-GAT1-0min-rep1.2x20mers.unique.bam OUTPUT=L939-GAT1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L939-GAT1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L940-SKO1-0min-rep1.2x20mers.unique.bam OUTPUT=L940-SKO1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L940-SKO1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L941-CHA4-0min-rep1.2x20mers.unique.bam OUTPUT=L941-CHA4-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L941-CHA4-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L942-PHO2-0min-rep1.2x20mers.unique.bam OUTPUT=L942-PHO2-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L942-PHO2-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L943-ROX1-0min-rep1.2x20mers.unique.bam OUTPUT=L943-ROX1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L943-ROX1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L944-HOT1-0min-rep1.2x20mers.unique.bam OUTPUT=L944-HOT1-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L944-HOT1-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L945-YAP5-0min-rep1.2x20mers.unique.bam OUTPUT=L945-YAP5-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L945-YAP5-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L946-GAT4-0min-rep1.2x20mers.unique.bam OUTPUT=L946-GAT4-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L946-GAT4-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L947-SKN7-0min-rep1.2x20mers.unique.bam OUTPUT=L947-SKN7-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L947-SKN7-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L948-MSN4-0min-rep1.2x20mers.unique.bam OUTPUT=L948-MSN4-0min-rep1.2x20mers.unique.dedup.bam METRICS_FILE=L948-MSN4-0min-rep1.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L973-HOT1-0min-rep2.2x20mers.unique.bam OUTPUT=L973-HOT1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L973-HOT1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L974-ROX1-0min-rep2.2x20mers.unique.bam OUTPUT=L974-ROX1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L974-ROX1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L975-PHO2-0min-rep2.2x20mers.unique.bam OUTPUT=L975-PHO2-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L975-PHO2-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L976-CHA4-0min-rep2.2x20mers.unique.bam OUTPUT=L976-CHA4-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L976-CHA4-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L977-GAT4-0min-rep2.2x20mers.unique.bam OUTPUT=L977-GAT4-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L977-GAT4-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L978-YAP5-0min-rep2.2x20mers.unique.bam OUTPUT=L978-YAP5-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L978-YAP5-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L979-MSN2-0min-rep2.2x20mers.unique.bam OUTPUT=L979-MSN2-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L979-MSN2-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L980-BDF1-0min-rep2.2x20mers.unique.bam OUTPUT=L980-BDF1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L980-BDF1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L981-SFP1-0min-rep2.2x20mers.unique.bam OUTPUT=L981-SFP1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L981-SFP1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L982-SKN7-0min-rep2.2x20mers.unique.bam OUTPUT=L982-SKN7-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L982-SKN7-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L983-PDR3-0min-rep2.2x20mers.unique.bam OUTPUT=L983-PDR3-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L983-PDR3-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L984-HOG1-0min-rep2.2x20mers.unique.bam OUTPUT=L984-HOG1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L984-HOG1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L985-YAP3-0min-rep2.2x20mers.unique.bam OUTPUT=L985-YAP3-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L985-YAP3-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L986-MSN1-0min-rep2.2x20mers.unique.bam OUTPUT=L986-MSN1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L986-MSN1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L987-MSN4-0min-rep2.2x20mers.unique.bam OUTPUT=L987-MSN4-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L987-MSN4-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L988-YAP6-0min-rep2.2x20mers.unique.bam OUTPUT=L988-YAP6-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L988-YAP6-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L989-YAP1-0min-rep2.2x20mers.unique.bam OUTPUT=L989-YAP1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L989-YAP1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L990-SMP1-0min-rep2.2x20mers.unique.bam OUTPUT=L990-SMP1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L990-SMP1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L991-ARR1-0min-rep2.2x20mers.unique.bam OUTPUT=L991-ARR1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L991-ARR1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L992-UME6-0min-rep2.2x20mers.unique.bam OUTPUT=L992-UME6-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L992-UME6-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L993-PHO4-0min-rep2.2x20mers.unique.bam OUTPUT=L993-PHO4-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L993-PHO4-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L994-SKO1-0min-rep2.2x20mers.unique.bam OUTPUT=L994-SKO1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L994-SKO1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L995-YAP7-0min-rep2.2x20mers.unique.bam OUTPUT=L995-YAP7-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L995-YAP7-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L996-GAT1-0min-rep2.2x20mers.unique.bam OUTPUT=L996-GAT1-0min-rep2.2x20mers.unique.dedup.bam METRICS_FILE=L996-GAT1-0min-rep2.2x20mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x15mers.unique.bam OUTPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x15mers.unique.dedup.bam METRICS_FILE=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x15mers.unique.bam OUTPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x15mers.unique.dedup.bam METRICS_FILE=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x15mers.unique.bam OUTPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x15mers.unique.dedup.bam METRICS_FILE=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x15mers.unique.bam OUTPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x15mers.unique.dedup.bam METRICS_FILE=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x15mers.unique.bam OUTPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x15mers.unique.dedup.bam METRICS_FILE=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x15mers.unique.bam OUTPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x15mers.unique.dedup.bam METRICS_FILE=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x15mers.unique.bam OUTPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x15mers.unique.dedup.bam METRICS_FILE=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x15mers.unique.bam OUTPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x15mers.unique.dedup.bam METRICS_FILE=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x15mers.unique.bam OUTPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x15mers.unique.dedup.bam METRICS_FILE=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x15mers.unique.bam OUTPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x15mers.unique.dedup.bam METRICS_FILE=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x15mers.unique.bam OUTPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x15mers.unique.dedup.bam METRICS_FILE=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x15mers.unique.bam OUTPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x15mers.unique.dedup.bam METRICS_FILE=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x15mers.unique.bam OUTPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x15mers.unique.dedup.bam METRICS_FILE=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x15mers.unique.bam OUTPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x15mers.unique.dedup.bam METRICS_FILE=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x15mers.unique.bam OUTPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x15mers.unique.dedup.bam METRICS_FILE=L1062-Training_camp_33-WT-0min-rep2-srstern.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x15mers.unique.bam OUTPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x15mers.unique.dedup.bam METRICS_FILE=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x15mers.unique.bam OUTPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x15mers.unique.dedup.bam METRICS_FILE=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x15mers.unique.bam OUTPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x15mers.unique.dedup.bam METRICS_FILE=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L665-FUN30.2x15mers.unique.bam OUTPUT=L665-FUN30.2x15mers.unique.dedup.bam METRICS_FILE=L665-FUN30.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L666-MSS11.2x15mers.unique.bam OUTPUT=L666-MSS11.2x15mers.unique.dedup.bam METRICS_FILE=L666-MSS11.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L667-YAP7.2x15mers.unique.bam OUTPUT=L667-YAP7.2x15mers.unique.dedup.bam METRICS_FILE=L667-YAP7.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L668-CUP9.2x15mers.unique.bam OUTPUT=L668-CUP9.2x15mers.unique.dedup.bam METRICS_FILE=L668-CUP9.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L669-ARG80.2x15mers.unique.bam OUTPUT=L669-ARG80.2x15mers.unique.dedup.bam METRICS_FILE=L669-ARG80.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L670-ARP6.2x15mers.unique.bam OUTPUT=L670-ARP6.2x15mers.unique.dedup.bam METRICS_FILE=L670-ARP6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L671-HAP5.2x15mers.unique.bam OUTPUT=L671-HAP5.2x15mers.unique.dedup.bam METRICS_FILE=L671-HAP5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L672-CAT8.2x15mers.unique.bam OUTPUT=L672-CAT8.2x15mers.unique.dedup.bam METRICS_FILE=L672-CAT8.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L673-RDS2.2x15mers.unique.bam OUTPUT=L673-RDS2.2x15mers.unique.dedup.bam METRICS_FILE=L673-RDS2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L674-CIN5.2x15mers.unique.bam OUTPUT=L674-CIN5.2x15mers.unique.dedup.bam METRICS_FILE=L674-CIN5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L675-RDR1.2x15mers.unique.bam OUTPUT=L675-RDR1.2x15mers.unique.dedup.bam METRICS_FILE=L675-RDR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L676-AFT2.2x15mers.unique.bam OUTPUT=L676-AFT2.2x15mers.unique.dedup.bam METRICS_FILE=L676-AFT2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L677-YAP1.2x15mers.unique.bam OUTPUT=L677-YAP1.2x15mers.unique.dedup.bam METRICS_FILE=L677-YAP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L678-IOC2.2x15mers.unique.bam OUTPUT=L678-IOC2.2x15mers.unique.dedup.bam METRICS_FILE=L678-IOC2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L679-MAC1.2x15mers.unique.bam OUTPUT=L679-MAC1.2x15mers.unique.dedup.bam METRICS_FILE=L679-MAC1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L680-RTG1.2x15mers.unique.bam OUTPUT=L680-RTG1.2x15mers.unique.dedup.bam METRICS_FILE=L680-RTG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L681-RGM1.2x15mers.unique.bam OUTPUT=L681-RGM1.2x15mers.unique.dedup.bam METRICS_FILE=L681-RGM1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L682-ERT1.2x15mers.unique.bam OUTPUT=L682-ERT1.2x15mers.unique.dedup.bam METRICS_FILE=L682-ERT1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L683-TYE7.2x15mers.unique.bam OUTPUT=L683-TYE7.2x15mers.unique.dedup.bam METRICS_FILE=L683-TYE7.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L684-DAL82.2x15mers.unique.bam OUTPUT=L684-DAL82.2x15mers.unique.dedup.bam METRICS_FILE=L684-DAL82.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L685-TEA1.2x15mers.unique.bam OUTPUT=L685-TEA1.2x15mers.unique.dedup.bam METRICS_FILE=L685-TEA1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L686-USV1.2x15mers.unique.bam OUTPUT=L686-USV1.2x15mers.unique.dedup.bam METRICS_FILE=L686-USV1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L687-SMP1.2x15mers.unique.bam OUTPUT=L687-SMP1.2x15mers.unique.dedup.bam METRICS_FILE=L687-SMP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L688-ABF2.2x15mers.unique.bam OUTPUT=L688-ABF2.2x15mers.unique.dedup.bam METRICS_FILE=L688-ABF2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L689-MBP1.2x15mers.unique.bam OUTPUT=L689-MBP1.2x15mers.unique.dedup.bam METRICS_FILE=L689-MBP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L690-CRZ1.2x15mers.unique.bam OUTPUT=L690-CRZ1.2x15mers.unique.dedup.bam METRICS_FILE=L690-CRZ1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L691-FKH2.2x15mers.unique.bam OUTPUT=L691-FKH2.2x15mers.unique.dedup.bam METRICS_FILE=L691-FKH2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L692-GAT4.2x15mers.unique.bam OUTPUT=L692-GAT4.2x15mers.unique.dedup.bam METRICS_FILE=L692-GAT4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L693-STP4.2x15mers.unique.bam OUTPUT=L693-STP4.2x15mers.unique.dedup.bam METRICS_FILE=L693-STP4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L694-IOC3.2x15mers.unique.bam OUTPUT=L694-IOC3.2x15mers.unique.dedup.bam METRICS_FILE=L694-IOC3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L695-NRG2.2x15mers.unique.bam OUTPUT=L695-NRG2.2x15mers.unique.dedup.bam METRICS_FILE=L695-NRG2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L697-CST9.2x15mers.unique.bam OUTPUT=L697-CST9.2x15mers.unique.dedup.bam METRICS_FILE=L697-CST9.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L698-CST6.2x15mers.unique.bam OUTPUT=L698-CST6.2x15mers.unique.dedup.bam METRICS_FILE=L698-CST6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L699-WAR1.2x15mers.unique.bam OUTPUT=L699-WAR1.2x15mers.unique.dedup.bam METRICS_FILE=L699-WAR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L701-DAL80.2x15mers.unique.bam OUTPUT=L701-DAL80.2x15mers.unique.dedup.bam METRICS_FILE=L701-DAL80.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L702-SIR2.2x15mers.unique.bam OUTPUT=L702-SIR2.2x15mers.unique.dedup.bam METRICS_FILE=L702-SIR2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L704-REC8.2x15mers.unique.bam OUTPUT=L704-REC8.2x15mers.unique.dedup.bam METRICS_FILE=L704-REC8.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L705-TBS1.2x15mers.unique.bam OUTPUT=L705-TBS1.2x15mers.unique.dedup.bam METRICS_FILE=L705-TBS1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L706-URC2.2x15mers.unique.bam OUTPUT=L706-URC2.2x15mers.unique.dedup.bam METRICS_FILE=L706-URC2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L708-HDA1.2x15mers.unique.bam OUTPUT=L708-HDA1.2x15mers.unique.dedup.bam METRICS_FILE=L708-HDA1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L710-ASG1.2x15mers.unique.bam OUTPUT=L710-ASG1.2x15mers.unique.dedup.bam METRICS_FILE=L710-ASG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L713-YNR063W.2x15mers.unique.bam OUTPUT=L713-YNR063W.2x15mers.unique.dedup.bam METRICS_FILE=L713-YNR063W.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L716-HOG1.2x15mers.unique.bam OUTPUT=L716-HOG1.2x15mers.unique.dedup.bam METRICS_FILE=L716-HOG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L717-DOT6.2x15mers.unique.bam OUTPUT=L717-DOT6.2x15mers.unique.dedup.bam METRICS_FILE=L717-DOT6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L718-MSN1.2x15mers.unique.bam OUTPUT=L718-MSN1.2x15mers.unique.dedup.bam METRICS_FILE=L718-MSN1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L720-INO4.2x15mers.unique.bam OUTPUT=L720-INO4.2x15mers.unique.dedup.bam METRICS_FILE=L720-INO4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L721-BYE1.2x15mers.unique.bam OUTPUT=L721-BYE1.2x15mers.unique.dedup.bam METRICS_FILE=L721-BYE1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L722-LSM1.2x15mers.unique.bam OUTPUT=L722-LSM1.2x15mers.unique.dedup.bam METRICS_FILE=L722-LSM1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L723-YER064C.2x15mers.unique.bam OUTPUT=L723-YER064C.2x15mers.unique.dedup.bam METRICS_FILE=L723-YER064C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L725-YFL052W.2x15mers.unique.bam OUTPUT=L725-YFL052W.2x15mers.unique.dedup.bam METRICS_FILE=L725-YFL052W.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L726-HAL9.2x15mers.unique.bam OUTPUT=L726-HAL9.2x15mers.unique.dedup.bam METRICS_FILE=L726-HAL9.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L727-RPH1.2x15mers.unique.bam OUTPUT=L727-RPH1.2x15mers.unique.dedup.bam METRICS_FILE=L727-RPH1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L730-GAT1.2x15mers.unique.bam OUTPUT=L730-GAT1.2x15mers.unique.dedup.bam METRICS_FILE=L730-GAT1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L732-YER130C.2x15mers.unique.bam OUTPUT=L732-YER130C.2x15mers.unique.dedup.bam METRICS_FILE=L732-YER130C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L733-RTG3.2x15mers.unique.bam OUTPUT=L733-RTG3.2x15mers.unique.dedup.bam METRICS_FILE=L733-RTG3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L734-SWI4.2x15mers.unique.bam OUTPUT=L734-SWI4.2x15mers.unique.dedup.bam METRICS_FILE=L734-SWI4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L735-RPN4.2x15mers.unique.bam OUTPUT=L735-RPN4.2x15mers.unique.dedup.bam METRICS_FILE=L735-RPN4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L736-SPO11.2x15mers.unique.bam OUTPUT=L736-SPO11.2x15mers.unique.dedup.bam METRICS_FILE=L736-SPO11.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L737-STB5.2x15mers.unique.bam OUTPUT=L737-STB5.2x15mers.unique.dedup.bam METRICS_FILE=L737-STB5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L738-NDT80.2x15mers.unique.bam OUTPUT=L738-NDT80.2x15mers.unique.dedup.bam METRICS_FILE=L738-NDT80.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L739-GIS1.2x15mers.unique.bam OUTPUT=L739-GIS1.2x15mers.unique.dedup.bam METRICS_FILE=L739-GIS1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L740-LEU3.2x15mers.unique.bam OUTPUT=L740-LEU3.2x15mers.unique.dedup.bam METRICS_FILE=L740-LEU3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L741-YAP3.2x15mers.unique.bam OUTPUT=L741-YAP3.2x15mers.unique.dedup.bam METRICS_FILE=L741-YAP3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L742-NRG1.2x15mers.unique.bam OUTPUT=L742-NRG1.2x15mers.unique.dedup.bam METRICS_FILE=L742-NRG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L743-MSN4.2x15mers.unique.bam OUTPUT=L743-MSN4.2x15mers.unique.dedup.bam METRICS_FILE=L743-MSN4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L744-ASH1.2x15mers.unique.bam OUTPUT=L744-ASH1.2x15mers.unique.dedup.bam METRICS_FILE=L744-ASH1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L745-HAP4.2x15mers.unique.bam OUTPUT=L745-HAP4.2x15mers.unique.dedup.bam METRICS_FILE=L745-HAP4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L746-HPC2.2x15mers.unique.bam OUTPUT=L746-HPC2.2x15mers.unique.dedup.bam METRICS_FILE=L746-HPC2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L747-TOS8.2x15mers.unique.bam OUTPUT=L747-TOS8.2x15mers.unique.dedup.bam METRICS_FILE=L747-TOS8.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L748-HOT1.2x15mers.unique.bam OUTPUT=L748-HOT1.2x15mers.unique.dedup.bam METRICS_FILE=L748-HOT1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L749-KAR4.2x15mers.unique.bam OUTPUT=L749-KAR4.2x15mers.unique.dedup.bam METRICS_FILE=L749-KAR4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L750-AZF1.2x15mers.unique.bam OUTPUT=L750-AZF1.2x15mers.unique.dedup.bam METRICS_FILE=L750-AZF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L751-ELG1.2x15mers.unique.bam OUTPUT=L751-ELG1.2x15mers.unique.dedup.bam METRICS_FILE=L751-ELG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L752-YGR067C.2x15mers.unique.bam OUTPUT=L752-YGR067C.2x15mers.unique.dedup.bam METRICS_FILE=L752-YGR067C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L753-unknown.2x15mers.unique.bam OUTPUT=L753-unknown.2x15mers.unique.dedup.bam METRICS_FILE=L753-unknown.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L754-LYS14.2x15mers.unique.bam OUTPUT=L754-LYS14.2x15mers.unique.dedup.bam METRICS_FILE=L754-LYS14.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L755-HIR3.2x15mers.unique.bam OUTPUT=L755-HIR3.2x15mers.unique.dedup.bam METRICS_FILE=L755-HIR3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L756-STB4.2x15mers.unique.bam OUTPUT=L756-STB4.2x15mers.unique.dedup.bam METRICS_FILE=L756-STB4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L757-KTI12.2x15mers.unique.bam OUTPUT=L757-KTI12.2x15mers.unique.dedup.bam METRICS_FILE=L757-KTI12.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L758-SKN7.2x15mers.unique.bam OUTPUT=L758-SKN7.2x15mers.unique.dedup.bam METRICS_FILE=L758-SKN7.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L759-RME1.2x15mers.unique.bam OUTPUT=L759-RME1.2x15mers.unique.dedup.bam METRICS_FILE=L759-RME1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L760-ISW1.2x15mers.unique.bam OUTPUT=L760-ISW1.2x15mers.unique.dedup.bam METRICS_FILE=L760-ISW1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L761-FZF1.2x15mers.unique.bam OUTPUT=L761-FZF1.2x15mers.unique.dedup.bam METRICS_FILE=L761-FZF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L762-SIP4.2x15mers.unique.bam OUTPUT=L762-SIP4.2x15mers.unique.dedup.bam METRICS_FILE=L762-SIP4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L763-PUT3.2x15mers.unique.bam OUTPUT=L763-PUT3.2x15mers.unique.dedup.bam METRICS_FILE=L763-PUT3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L764-STP2.2x15mers.unique.bam OUTPUT=L764-STP2.2x15mers.unique.dedup.bam METRICS_FILE=L764-STP2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L765-GZF3.2x15mers.unique.bam OUTPUT=L765-GZF3.2x15mers.unique.dedup.bam METRICS_FILE=L765-GZF3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L766-BAS1.2x15mers.unique.bam OUTPUT=L766-BAS1.2x15mers.unique.dedup.bam METRICS_FILE=L766-BAS1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L767-SUT2.2x15mers.unique.bam OUTPUT=L767-SUT2.2x15mers.unique.dedup.bam METRICS_FILE=L767-SUT2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L768-ROX1.2x15mers.unique.bam OUTPUT=L768-ROX1.2x15mers.unique.dedup.bam METRICS_FILE=L768-ROX1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L769-LIF1.2x15mers.unique.bam OUTPUT=L769-LIF1.2x15mers.unique.dedup.bam METRICS_FILE=L769-LIF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L770-THO1.2x15mers.unique.bam OUTPUT=L770-THO1.2x15mers.unique.dedup.bam METRICS_FILE=L770-THO1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L771-HDA2.2x15mers.unique.bam OUTPUT=L771-HDA2.2x15mers.unique.dedup.bam METRICS_FILE=L771-HDA2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L772-NUP170.2x15mers.unique.bam OUTPUT=L772-NUP170.2x15mers.unique.dedup.bam METRICS_FILE=L772-NUP170.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L773-YPR015C.2x15mers.unique.bam OUTPUT=L773-YPR015C.2x15mers.unique.dedup.bam METRICS_FILE=L773-YPR015C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L774-SUB1.2x15mers.unique.bam OUTPUT=L774-SUB1.2x15mers.unique.dedup.bam METRICS_FILE=L774-SUB1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L775-IME1.2x15mers.unique.bam OUTPUT=L775-IME1.2x15mers.unique.dedup.bam METRICS_FILE=L775-IME1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L776-HIR1.2x15mers.unique.bam OUTPUT=L776-HIR1.2x15mers.unique.dedup.bam METRICS_FILE=L776-HIR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L777-MET32.2x15mers.unique.bam OUTPUT=L777-MET32.2x15mers.unique.dedup.bam METRICS_FILE=L777-MET32.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L778-RLM1.2x15mers.unique.bam OUTPUT=L778-RLM1.2x15mers.unique.dedup.bam METRICS_FILE=L778-RLM1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L779-YTA7.2x15mers.unique.bam OUTPUT=L779-YTA7.2x15mers.unique.dedup.bam METRICS_FILE=L779-YTA7.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L780-HIR2.2x15mers.unique.bam OUTPUT=L780-HIR2.2x15mers.unique.dedup.bam METRICS_FILE=L780-HIR2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L781-ZAP1.2x15mers.unique.bam OUTPUT=L781-ZAP1.2x15mers.unique.dedup.bam METRICS_FILE=L781-ZAP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L782-RDS1.2x15mers.unique.bam OUTPUT=L782-RDS1.2x15mers.unique.dedup.bam METRICS_FILE=L782-RDS1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L783-BDF1.2x15mers.unique.bam OUTPUT=L783-BDF1.2x15mers.unique.dedup.bam METRICS_FILE=L783-BDF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L784-HDA3.2x15mers.unique.bam OUTPUT=L784-HDA3.2x15mers.unique.dedup.bam METRICS_FILE=L784-HDA3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L785-CAD1.2x15mers.unique.bam OUTPUT=L785-CAD1.2x15mers.unique.dedup.bam METRICS_FILE=L785-CAD1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L786-SIR4.2x15mers.unique.bam OUTPUT=L786-SIR4.2x15mers.unique.dedup.bam METRICS_FILE=L786-SIR4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L787-REF2.2x15mers.unique.bam OUTPUT=L787-REF2.2x15mers.unique.dedup.bam METRICS_FILE=L787-REF2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L788-MET31.2x15mers.unique.bam OUTPUT=L788-MET31.2x15mers.unique.dedup.bam METRICS_FILE=L788-MET31.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L789-ARO80.2x15mers.unique.bam OUTPUT=L789-ARO80.2x15mers.unique.dedup.bam METRICS_FILE=L789-ARO80.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L790-RSF2.2x15mers.unique.bam OUTPUT=L790-RSF2.2x15mers.unique.dedup.bam METRICS_FILE=L790-RSF2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L791-CTF4.2x15mers.unique.bam OUTPUT=L791-CTF4.2x15mers.unique.dedup.bam METRICS_FILE=L791-CTF4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L792-CDC73.2x15mers.unique.bam OUTPUT=L792-CDC73.2x15mers.unique.dedup.bam METRICS_FILE=L792-CDC73.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L793-OAF1.2x15mers.unique.bam OUTPUT=L793-OAF1.2x15mers.unique.dedup.bam METRICS_FILE=L793-OAF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L794-UPC2.2x15mers.unique.bam OUTPUT=L794-UPC2.2x15mers.unique.dedup.bam METRICS_FILE=L794-UPC2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L795-MIG3.2x15mers.unique.bam OUTPUT=L795-MIG3.2x15mers.unique.dedup.bam METRICS_FILE=L795-MIG3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L796-UME6.2x15mers.unique.bam OUTPUT=L796-UME6.2x15mers.unique.dedup.bam METRICS_FILE=L796-UME6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L797-REI1.2x15mers.unique.bam OUTPUT=L797-REI1.2x15mers.unique.dedup.bam METRICS_FILE=L797-REI1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L798-YLR278C.2x15mers.unique.bam OUTPUT=L798-YLR278C.2x15mers.unique.dedup.bam METRICS_FILE=L798-YLR278C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L799-SFP1.2x15mers.unique.bam OUTPUT=L799-SFP1.2x15mers.unique.dedup.bam METRICS_FILE=L799-SFP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L800-ECM23.2x15mers.unique.bam OUTPUT=L800-ECM23.2x15mers.unique.dedup.bam METRICS_FILE=L800-ECM23.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L801-VHR1.2x15mers.unique.bam OUTPUT=L801-VHR1.2x15mers.unique.dedup.bam METRICS_FILE=L801-VHR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L802-DHH1.2x15mers.unique.bam OUTPUT=L802-DHH1.2x15mers.unique.dedup.bam METRICS_FILE=L802-DHH1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L803-YAP6.2x15mers.unique.bam OUTPUT=L803-YAP6.2x15mers.unique.dedup.bam METRICS_FILE=L803-YAP6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L804-GCN4.2x15mers.unique.bam OUTPUT=L804-GCN4.2x15mers.unique.dedup.bam METRICS_FILE=L804-GCN4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L805-PDR1.2x15mers.unique.bam OUTPUT=L805-PDR1.2x15mers.unique.dedup.bam METRICS_FILE=L805-PDR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L806-MIG2.2x15mers.unique.bam OUTPUT=L806-MIG2.2x15mers.unique.dedup.bam METRICS_FILE=L806-MIG2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L807-ADR1.2x15mers.unique.bam OUTPUT=L807-ADR1.2x15mers.unique.dedup.bam METRICS_FILE=L807-ADR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L808-YPR022C.2x15mers.unique.bam OUTPUT=L808-YPR022C.2x15mers.unique.dedup.bam METRICS_FILE=L808-YPR022C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L809-HAA1.2x15mers.unique.bam OUTPUT=L809-HAA1.2x15mers.unique.dedup.bam METRICS_FILE=L809-HAA1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L810-ARR1.2x15mers.unique.bam OUTPUT=L810-ARR1.2x15mers.unique.dedup.bam METRICS_FILE=L810-ARR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L811-YPR013C.2x15mers.unique.bam OUTPUT=L811-YPR013C.2x15mers.unique.dedup.bam METRICS_FILE=L811-YPR013C.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L812-RGT1.2x15mers.unique.bam OUTPUT=L812-RGT1.2x15mers.unique.dedup.bam METRICS_FILE=L812-RGT1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L813-RFX1.2x15mers.unique.bam OUTPUT=L813-RFX1.2x15mers.unique.dedup.bam METRICS_FILE=L813-RFX1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L814-IXR1.2x15mers.unique.bam OUTPUT=L814-IXR1.2x15mers.unique.dedup.bam METRICS_FILE=L814-IXR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L815-PDR8.2x15mers.unique.bam OUTPUT=L815-PDR8.2x15mers.unique.dedup.bam METRICS_FILE=L815-PDR8.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L816-ECM22.2x15mers.unique.bam OUTPUT=L816-ECM22.2x15mers.unique.dedup.bam METRICS_FILE=L816-ECM22.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L817-XRN1.2x15mers.unique.bam OUTPUT=L817-XRN1.2x15mers.unique.dedup.bam METRICS_FILE=L817-XRN1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L818-YRR1.2x15mers.unique.bam OUTPUT=L818-YRR1.2x15mers.unique.dedup.bam METRICS_FILE=L818-YRR1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L819-MSN2.2x15mers.unique.bam OUTPUT=L819-MSN2.2x15mers.unique.dedup.bam METRICS_FILE=L819-MSN2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L820-YPR196W.2x15mers.unique.bam OUTPUT=L820-YPR196W.2x15mers.unique.dedup.bam METRICS_FILE=L820-YPR196W.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L821-DAL81.2x15mers.unique.bam OUTPUT=L821-DAL81.2x15mers.unique.dedup.bam METRICS_FILE=L821-DAL81.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L822-HAT1.2x15mers.unique.bam OUTPUT=L822-HAT1.2x15mers.unique.dedup.bam METRICS_FILE=L822-HAT1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L823-PAF1.2x15mers.unique.bam OUTPUT=L823-PAF1.2x15mers.unique.dedup.bam METRICS_FILE=L823-PAF1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L824-NHP10.2x15mers.unique.bam OUTPUT=L824-NHP10.2x15mers.unique.dedup.bam METRICS_FILE=L824-NHP10.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L825-SPP1.2x15mers.unique.bam OUTPUT=L825-SPP1.2x15mers.unique.dedup.bam METRICS_FILE=L825-SPP1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L826-SFL1.2x15mers.unique.bam OUTPUT=L826-SFL1.2x15mers.unique.dedup.bam METRICS_FILE=L826-SFL1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L827-STP3.2x15mers.unique.bam OUTPUT=L827-STP3.2x15mers.unique.dedup.bam METRICS_FILE=L827-STP3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L828-YRM1.2x15mers.unique.bam OUTPUT=L828-YRM1.2x15mers.unique.dedup.bam METRICS_FILE=L828-YRM1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L829-ISW2.2x15mers.unique.bam OUTPUT=L829-ISW2.2x15mers.unique.dedup.bam METRICS_FILE=L829-ISW2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L830-HTZ1.2x15mers.unique.bam OUTPUT=L830-HTZ1.2x15mers.unique.dedup.bam METRICS_FILE=L830-HTZ1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L831-PHD1.2x15mers.unique.bam OUTPUT=L831-PHD1.2x15mers.unique.dedup.bam METRICS_FILE=L831-PHD1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L832-SWI5.2x15mers.unique.bam OUTPUT=L832-SWI5.2x15mers.unique.dedup.bam METRICS_FILE=L832-SWI5.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L833-ACA1.2x15mers.unique.bam OUTPUT=L833-ACA1.2x15mers.unique.dedup.bam METRICS_FILE=L833-ACA1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L834-INO2.2x15mers.unique.bam OUTPUT=L834-INO2.2x15mers.unique.dedup.bam METRICS_FILE=L834-INO2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L835-PHO4.2x15mers.unique.bam OUTPUT=L835-PHO4.2x15mers.unique.dedup.bam METRICS_FILE=L835-PHO4.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L836-MGA1.2x15mers.unique.bam OUTPUT=L836-MGA1.2x15mers.unique.dedup.bam METRICS_FILE=L836-MGA1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L837-MIG1.2x15mers.unique.bam OUTPUT=L837-MIG1.2x15mers.unique.dedup.bam METRICS_FILE=L837-MIG1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L838-HAP3.2x15mers.unique.bam OUTPUT=L838-HAP3.2x15mers.unique.dedup.bam METRICS_FILE=L838-HAP3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L839-YHR177W.2x15mers.unique.bam OUTPUT=L839-YHR177W.2x15mers.unique.dedup.bam METRICS_FILE=L839-YHR177W.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L847-GLN3.2x15mers.unique.bam OUTPUT=L847-GLN3.2x15mers.unique.dedup.bam METRICS_FILE=L847-GLN3.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L848-TOD6.2x15mers.unique.bam OUTPUT=L848-TOD6.2x15mers.unique.dedup.bam METRICS_FILE=L848-TOD6.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L925-MSN2-0min-rep1.2x15mers.unique.bam OUTPUT=L925-MSN2-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L925-MSN2-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L927-MSN1-0min-rep1.2x15mers.unique.bam OUTPUT=L927-MSN1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L927-MSN1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L928-HOG1-0min-rep1.2x15mers.unique.bam OUTPUT=L928-HOG1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L928-HOG1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L929-BDF1-0min-rep1.2x15mers.unique.bam OUTPUT=L929-BDF1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L929-BDF1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L930-YAP7-0min-rep1.2x15mers.unique.bam OUTPUT=L930-YAP7-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L930-YAP7-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L931-UME6-0min-rep1.2x15mers.unique.bam OUTPUT=L931-UME6-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L931-UME6-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L932-SMP1-0min-rep1.2x15mers.unique.bam OUTPUT=L932-SMP1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L932-SMP1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L933-YAP1-0min-rep1.2x15mers.unique.bam OUTPUT=L933-YAP1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L933-YAP1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L934-YAP3-0min-rep1.2x15mers.unique.bam OUTPUT=L934-YAP3-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L934-YAP3-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L935-ARR1-0min-rep1.2x15mers.unique.bam OUTPUT=L935-ARR1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L935-ARR1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L936-PHO4-0min-rep1.2x15mers.unique.bam OUTPUT=L936-PHO4-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L936-PHO4-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L937-YAP6-0min-rep1.2x15mers.unique.bam OUTPUT=L937-YAP6-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L937-YAP6-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L938-PDR3-0min-rep1.2x15mers.unique.bam OUTPUT=L938-PDR3-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L938-PDR3-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L939-GAT1-0min-rep1.2x15mers.unique.bam OUTPUT=L939-GAT1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L939-GAT1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L940-SKO1-0min-rep1.2x15mers.unique.bam OUTPUT=L940-SKO1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L940-SKO1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L941-CHA4-0min-rep1.2x15mers.unique.bam OUTPUT=L941-CHA4-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L941-CHA4-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L942-PHO2-0min-rep1.2x15mers.unique.bam OUTPUT=L942-PHO2-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L942-PHO2-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L943-ROX1-0min-rep1.2x15mers.unique.bam OUTPUT=L943-ROX1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L943-ROX1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L944-HOT1-0min-rep1.2x15mers.unique.bam OUTPUT=L944-HOT1-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L944-HOT1-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L945-YAP5-0min-rep1.2x15mers.unique.bam OUTPUT=L945-YAP5-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L945-YAP5-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L946-GAT4-0min-rep1.2x15mers.unique.bam OUTPUT=L946-GAT4-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L946-GAT4-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L947-SKN7-0min-rep1.2x15mers.unique.bam OUTPUT=L947-SKN7-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L947-SKN7-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L948-MSN4-0min-rep1.2x15mers.unique.bam OUTPUT=L948-MSN4-0min-rep1.2x15mers.unique.dedup.bam METRICS_FILE=L948-MSN4-0min-rep1.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L973-HOT1-0min-rep2.2x15mers.unique.bam OUTPUT=L973-HOT1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L973-HOT1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L974-ROX1-0min-rep2.2x15mers.unique.bam OUTPUT=L974-ROX1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L974-ROX1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L975-PHO2-0min-rep2.2x15mers.unique.bam OUTPUT=L975-PHO2-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L975-PHO2-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L976-CHA4-0min-rep2.2x15mers.unique.bam OUTPUT=L976-CHA4-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L976-CHA4-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L977-GAT4-0min-rep2.2x15mers.unique.bam OUTPUT=L977-GAT4-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L977-GAT4-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L978-YAP5-0min-rep2.2x15mers.unique.bam OUTPUT=L978-YAP5-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L978-YAP5-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L979-MSN2-0min-rep2.2x15mers.unique.bam OUTPUT=L979-MSN2-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L979-MSN2-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L980-BDF1-0min-rep2.2x15mers.unique.bam OUTPUT=L980-BDF1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L980-BDF1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L981-SFP1-0min-rep2.2x15mers.unique.bam OUTPUT=L981-SFP1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L981-SFP1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L982-SKN7-0min-rep2.2x15mers.unique.bam OUTPUT=L982-SKN7-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L982-SKN7-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L983-PDR3-0min-rep2.2x15mers.unique.bam OUTPUT=L983-PDR3-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L983-PDR3-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L984-HOG1-0min-rep2.2x15mers.unique.bam OUTPUT=L984-HOG1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L984-HOG1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L985-YAP3-0min-rep2.2x15mers.unique.bam OUTPUT=L985-YAP3-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L985-YAP3-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L986-MSN1-0min-rep2.2x15mers.unique.bam OUTPUT=L986-MSN1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L986-MSN1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L987-MSN4-0min-rep2.2x15mers.unique.bam OUTPUT=L987-MSN4-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L987-MSN4-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L988-YAP6-0min-rep2.2x15mers.unique.bam OUTPUT=L988-YAP6-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L988-YAP6-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L989-YAP1-0min-rep2.2x15mers.unique.bam OUTPUT=L989-YAP1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L989-YAP1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L990-SMP1-0min-rep2.2x15mers.unique.bam OUTPUT=L990-SMP1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L990-SMP1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L991-ARR1-0min-rep2.2x15mers.unique.bam OUTPUT=L991-ARR1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L991-ARR1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L992-UME6-0min-rep2.2x15mers.unique.bam OUTPUT=L992-UME6-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L992-UME6-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L993-PHO4-0min-rep2.2x15mers.unique.bam OUTPUT=L993-PHO4-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L993-PHO4-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L994-SKO1-0min-rep2.2x15mers.unique.bam OUTPUT=L994-SKO1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L994-SKO1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L995-YAP7-0min-rep2.2x15mers.unique.bam OUTPUT=L995-YAP7-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L995-YAP7-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L996-GAT1-0min-rep2.2x15mers.unique.bam OUTPUT=L996-GAT1-0min-rep2.2x15mers.unique.dedup.bam METRICS_FILE=L996-GAT1-0min-rep2.2x15mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x10mers.unique.bam OUTPUT=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x10mers.unique.dedup.bam METRICS_FILE=L1034-Training_camp_4-HOG1-0min-rep1-ajberg5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x10mers.unique.bam OUTPUT=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x10mers.unique.dedup.bam METRICS_FILE=L1035-Training_camp_5-YAP1-0min-rep2-annashch.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x10mers.unique.bam OUTPUT=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x10mers.unique.dedup.bam METRICS_FILE=L1037-Training_camp_7-MSN2-0min-rep2-annlin.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x10mers.unique.bam OUTPUT=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x10mers.unique.dedup.bam METRICS_FILE=L1040-Training_camp_10-MSN4-0min-rep2-clin5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x10mers.unique.bam OUTPUT=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x10mers.unique.dedup.bam METRICS_FILE=L1042-Training_camp_12-YAP1-0min-rep1-courtrun.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x10mers.unique.bam OUTPUT=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x10mers.unique.dedup.bam METRICS_FILE=L1043-Training_camp_13-MSN1-0min-rep2-cvduffy.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x10mers.unique.bam OUTPUT=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x10mers.unique.dedup.bam METRICS_FILE=L1045-Training_camp_15-WT-0min-rep1-genegra2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x10mers.unique.bam OUTPUT=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x10mers.unique.dedup.bam METRICS_FILE=L1048-Training_camp_18-SKN7-0min-rep2-jarhodes.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x10mers.unique.bam OUTPUT=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x10mers.unique.dedup.bam METRICS_FILE=L1050-Training_camp_20-MSN4-0min-rep1-lstrand.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x10mers.unique.bam OUTPUT=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x10mers.unique.dedup.bam METRICS_FILE=L1052-Training_camp_22-SKN7-0min-rep1-makena.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x10mers.unique.bam OUTPUT=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x10mers.unique.dedup.bam METRICS_FILE=L1055-Training_camp_26-HOG1-0min-rep2-miao1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x10mers.unique.bam OUTPUT=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x10mers.unique.dedup.bam METRICS_FILE=L1057-Training_camp_28-HOT1-0min-rep1-myhayes.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x10mers.unique.bam OUTPUT=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x10mers.unique.dedup.bam METRICS_FILE=L1058-Training_camp_29-MSN1-0min-rep1-sierrasb.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x10mers.unique.bam OUTPUT=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x10mers.unique.dedup.bam METRICS_FILE=L1061-Training_camp_32-HOT1-0min-rep2-soumyak.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x10mers.unique.bam OUTPUT=L1062-Training_camp_33-WT-0min-rep2-srstern.2x10mers.unique.dedup.bam METRICS_FILE=L1062-Training_camp_33-WT-0min-rep2-srstern.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x10mers.unique.bam OUTPUT=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x10mers.unique.dedup.bam METRICS_FILE=L1064-Training_camp_35-MSN2-0min-rep1-subkc.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x10mers.unique.bam OUTPUT=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x10mers.unique.dedup.bam METRICS_FILE=L1067-Training_camp_38-YAP7-0min-rep2-surag.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x10mers.unique.bam OUTPUT=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x10mers.unique.dedup.bam METRICS_FILE=L1068-Training_camp_39-YAP6-0min-rep2-zahoor.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L665-FUN30.2x10mers.unique.bam OUTPUT=L665-FUN30.2x10mers.unique.dedup.bam METRICS_FILE=L665-FUN30.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L666-MSS11.2x10mers.unique.bam OUTPUT=L666-MSS11.2x10mers.unique.dedup.bam METRICS_FILE=L666-MSS11.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L667-YAP7.2x10mers.unique.bam OUTPUT=L667-YAP7.2x10mers.unique.dedup.bam METRICS_FILE=L667-YAP7.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L668-CUP9.2x10mers.unique.bam OUTPUT=L668-CUP9.2x10mers.unique.dedup.bam METRICS_FILE=L668-CUP9.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L669-ARG80.2x10mers.unique.bam OUTPUT=L669-ARG80.2x10mers.unique.dedup.bam METRICS_FILE=L669-ARG80.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L670-ARP6.2x10mers.unique.bam OUTPUT=L670-ARP6.2x10mers.unique.dedup.bam METRICS_FILE=L670-ARP6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L671-HAP5.2x10mers.unique.bam OUTPUT=L671-HAP5.2x10mers.unique.dedup.bam METRICS_FILE=L671-HAP5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L672-CAT8.2x10mers.unique.bam OUTPUT=L672-CAT8.2x10mers.unique.dedup.bam METRICS_FILE=L672-CAT8.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L673-RDS2.2x10mers.unique.bam OUTPUT=L673-RDS2.2x10mers.unique.dedup.bam METRICS_FILE=L673-RDS2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L674-CIN5.2x10mers.unique.bam OUTPUT=L674-CIN5.2x10mers.unique.dedup.bam METRICS_FILE=L674-CIN5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L675-RDR1.2x10mers.unique.bam OUTPUT=L675-RDR1.2x10mers.unique.dedup.bam METRICS_FILE=L675-RDR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L676-AFT2.2x10mers.unique.bam OUTPUT=L676-AFT2.2x10mers.unique.dedup.bam METRICS_FILE=L676-AFT2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L677-YAP1.2x10mers.unique.bam OUTPUT=L677-YAP1.2x10mers.unique.dedup.bam METRICS_FILE=L677-YAP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L678-IOC2.2x10mers.unique.bam OUTPUT=L678-IOC2.2x10mers.unique.dedup.bam METRICS_FILE=L678-IOC2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L679-MAC1.2x10mers.unique.bam OUTPUT=L679-MAC1.2x10mers.unique.dedup.bam METRICS_FILE=L679-MAC1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L680-RTG1.2x10mers.unique.bam OUTPUT=L680-RTG1.2x10mers.unique.dedup.bam METRICS_FILE=L680-RTG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L681-RGM1.2x10mers.unique.bam OUTPUT=L681-RGM1.2x10mers.unique.dedup.bam METRICS_FILE=L681-RGM1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L682-ERT1.2x10mers.unique.bam OUTPUT=L682-ERT1.2x10mers.unique.dedup.bam METRICS_FILE=L682-ERT1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L683-TYE7.2x10mers.unique.bam OUTPUT=L683-TYE7.2x10mers.unique.dedup.bam METRICS_FILE=L683-TYE7.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L684-DAL82.2x10mers.unique.bam OUTPUT=L684-DAL82.2x10mers.unique.dedup.bam METRICS_FILE=L684-DAL82.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L685-TEA1.2x10mers.unique.bam OUTPUT=L685-TEA1.2x10mers.unique.dedup.bam METRICS_FILE=L685-TEA1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L686-USV1.2x10mers.unique.bam OUTPUT=L686-USV1.2x10mers.unique.dedup.bam METRICS_FILE=L686-USV1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L687-SMP1.2x10mers.unique.bam OUTPUT=L687-SMP1.2x10mers.unique.dedup.bam METRICS_FILE=L687-SMP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L688-ABF2.2x10mers.unique.bam OUTPUT=L688-ABF2.2x10mers.unique.dedup.bam METRICS_FILE=L688-ABF2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L689-MBP1.2x10mers.unique.bam OUTPUT=L689-MBP1.2x10mers.unique.dedup.bam METRICS_FILE=L689-MBP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L690-CRZ1.2x10mers.unique.bam OUTPUT=L690-CRZ1.2x10mers.unique.dedup.bam METRICS_FILE=L690-CRZ1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L691-FKH2.2x10mers.unique.bam OUTPUT=L691-FKH2.2x10mers.unique.dedup.bam METRICS_FILE=L691-FKH2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L692-GAT4.2x10mers.unique.bam OUTPUT=L692-GAT4.2x10mers.unique.dedup.bam METRICS_FILE=L692-GAT4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L693-STP4.2x10mers.unique.bam OUTPUT=L693-STP4.2x10mers.unique.dedup.bam METRICS_FILE=L693-STP4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L694-IOC3.2x10mers.unique.bam OUTPUT=L694-IOC3.2x10mers.unique.dedup.bam METRICS_FILE=L694-IOC3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L695-NRG2.2x10mers.unique.bam OUTPUT=L695-NRG2.2x10mers.unique.dedup.bam METRICS_FILE=L695-NRG2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L697-CST9.2x10mers.unique.bam OUTPUT=L697-CST9.2x10mers.unique.dedup.bam METRICS_FILE=L697-CST9.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L698-CST6.2x10mers.unique.bam OUTPUT=L698-CST6.2x10mers.unique.dedup.bam METRICS_FILE=L698-CST6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L699-WAR1.2x10mers.unique.bam OUTPUT=L699-WAR1.2x10mers.unique.dedup.bam METRICS_FILE=L699-WAR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L701-DAL80.2x10mers.unique.bam OUTPUT=L701-DAL80.2x10mers.unique.dedup.bam METRICS_FILE=L701-DAL80.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L702-SIR2.2x10mers.unique.bam OUTPUT=L702-SIR2.2x10mers.unique.dedup.bam METRICS_FILE=L702-SIR2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L704-REC8.2x10mers.unique.bam OUTPUT=L704-REC8.2x10mers.unique.dedup.bam METRICS_FILE=L704-REC8.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L705-TBS1.2x10mers.unique.bam OUTPUT=L705-TBS1.2x10mers.unique.dedup.bam METRICS_FILE=L705-TBS1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L706-URC2.2x10mers.unique.bam OUTPUT=L706-URC2.2x10mers.unique.dedup.bam METRICS_FILE=L706-URC2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L708-HDA1.2x10mers.unique.bam OUTPUT=L708-HDA1.2x10mers.unique.dedup.bam METRICS_FILE=L708-HDA1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L710-ASG1.2x10mers.unique.bam OUTPUT=L710-ASG1.2x10mers.unique.dedup.bam METRICS_FILE=L710-ASG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L713-YNR063W.2x10mers.unique.bam OUTPUT=L713-YNR063W.2x10mers.unique.dedup.bam METRICS_FILE=L713-YNR063W.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L716-HOG1.2x10mers.unique.bam OUTPUT=L716-HOG1.2x10mers.unique.dedup.bam METRICS_FILE=L716-HOG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L717-DOT6.2x10mers.unique.bam OUTPUT=L717-DOT6.2x10mers.unique.dedup.bam METRICS_FILE=L717-DOT6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L718-MSN1.2x10mers.unique.bam OUTPUT=L718-MSN1.2x10mers.unique.dedup.bam METRICS_FILE=L718-MSN1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L720-INO4.2x10mers.unique.bam OUTPUT=L720-INO4.2x10mers.unique.dedup.bam METRICS_FILE=L720-INO4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L721-BYE1.2x10mers.unique.bam OUTPUT=L721-BYE1.2x10mers.unique.dedup.bam METRICS_FILE=L721-BYE1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L722-LSM1.2x10mers.unique.bam OUTPUT=L722-LSM1.2x10mers.unique.dedup.bam METRICS_FILE=L722-LSM1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L723-YER064C.2x10mers.unique.bam OUTPUT=L723-YER064C.2x10mers.unique.dedup.bam METRICS_FILE=L723-YER064C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L725-YFL052W.2x10mers.unique.bam OUTPUT=L725-YFL052W.2x10mers.unique.dedup.bam METRICS_FILE=L725-YFL052W.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L726-HAL9.2x10mers.unique.bam OUTPUT=L726-HAL9.2x10mers.unique.dedup.bam METRICS_FILE=L726-HAL9.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L727-RPH1.2x10mers.unique.bam OUTPUT=L727-RPH1.2x10mers.unique.dedup.bam METRICS_FILE=L727-RPH1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L730-GAT1.2x10mers.unique.bam OUTPUT=L730-GAT1.2x10mers.unique.dedup.bam METRICS_FILE=L730-GAT1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L732-YER130C.2x10mers.unique.bam OUTPUT=L732-YER130C.2x10mers.unique.dedup.bam METRICS_FILE=L732-YER130C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L733-RTG3.2x10mers.unique.bam OUTPUT=L733-RTG3.2x10mers.unique.dedup.bam METRICS_FILE=L733-RTG3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L734-SWI4.2x10mers.unique.bam OUTPUT=L734-SWI4.2x10mers.unique.dedup.bam METRICS_FILE=L734-SWI4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L735-RPN4.2x10mers.unique.bam OUTPUT=L735-RPN4.2x10mers.unique.dedup.bam METRICS_FILE=L735-RPN4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L736-SPO11.2x10mers.unique.bam OUTPUT=L736-SPO11.2x10mers.unique.dedup.bam METRICS_FILE=L736-SPO11.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L737-STB5.2x10mers.unique.bam OUTPUT=L737-STB5.2x10mers.unique.dedup.bam METRICS_FILE=L737-STB5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L738-NDT80.2x10mers.unique.bam OUTPUT=L738-NDT80.2x10mers.unique.dedup.bam METRICS_FILE=L738-NDT80.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L739-GIS1.2x10mers.unique.bam OUTPUT=L739-GIS1.2x10mers.unique.dedup.bam METRICS_FILE=L739-GIS1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L740-LEU3.2x10mers.unique.bam OUTPUT=L740-LEU3.2x10mers.unique.dedup.bam METRICS_FILE=L740-LEU3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L741-YAP3.2x10mers.unique.bam OUTPUT=L741-YAP3.2x10mers.unique.dedup.bam METRICS_FILE=L741-YAP3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L742-NRG1.2x10mers.unique.bam OUTPUT=L742-NRG1.2x10mers.unique.dedup.bam METRICS_FILE=L742-NRG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L743-MSN4.2x10mers.unique.bam OUTPUT=L743-MSN4.2x10mers.unique.dedup.bam METRICS_FILE=L743-MSN4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L744-ASH1.2x10mers.unique.bam OUTPUT=L744-ASH1.2x10mers.unique.dedup.bam METRICS_FILE=L744-ASH1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L745-HAP4.2x10mers.unique.bam OUTPUT=L745-HAP4.2x10mers.unique.dedup.bam METRICS_FILE=L745-HAP4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L746-HPC2.2x10mers.unique.bam OUTPUT=L746-HPC2.2x10mers.unique.dedup.bam METRICS_FILE=L746-HPC2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L747-TOS8.2x10mers.unique.bam OUTPUT=L747-TOS8.2x10mers.unique.dedup.bam METRICS_FILE=L747-TOS8.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L748-HOT1.2x10mers.unique.bam OUTPUT=L748-HOT1.2x10mers.unique.dedup.bam METRICS_FILE=L748-HOT1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L749-KAR4.2x10mers.unique.bam OUTPUT=L749-KAR4.2x10mers.unique.dedup.bam METRICS_FILE=L749-KAR4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L750-AZF1.2x10mers.unique.bam OUTPUT=L750-AZF1.2x10mers.unique.dedup.bam METRICS_FILE=L750-AZF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L751-ELG1.2x10mers.unique.bam OUTPUT=L751-ELG1.2x10mers.unique.dedup.bam METRICS_FILE=L751-ELG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L752-YGR067C.2x10mers.unique.bam OUTPUT=L752-YGR067C.2x10mers.unique.dedup.bam METRICS_FILE=L752-YGR067C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L753-unknown.2x10mers.unique.bam OUTPUT=L753-unknown.2x10mers.unique.dedup.bam METRICS_FILE=L753-unknown.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L754-LYS14.2x10mers.unique.bam OUTPUT=L754-LYS14.2x10mers.unique.dedup.bam METRICS_FILE=L754-LYS14.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L755-HIR3.2x10mers.unique.bam OUTPUT=L755-HIR3.2x10mers.unique.dedup.bam METRICS_FILE=L755-HIR3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L756-STB4.2x10mers.unique.bam OUTPUT=L756-STB4.2x10mers.unique.dedup.bam METRICS_FILE=L756-STB4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L757-KTI12.2x10mers.unique.bam OUTPUT=L757-KTI12.2x10mers.unique.dedup.bam METRICS_FILE=L757-KTI12.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L758-SKN7.2x10mers.unique.bam OUTPUT=L758-SKN7.2x10mers.unique.dedup.bam METRICS_FILE=L758-SKN7.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L759-RME1.2x10mers.unique.bam OUTPUT=L759-RME1.2x10mers.unique.dedup.bam METRICS_FILE=L759-RME1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L760-ISW1.2x10mers.unique.bam OUTPUT=L760-ISW1.2x10mers.unique.dedup.bam METRICS_FILE=L760-ISW1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L761-FZF1.2x10mers.unique.bam OUTPUT=L761-FZF1.2x10mers.unique.dedup.bam METRICS_FILE=L761-FZF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L762-SIP4.2x10mers.unique.bam OUTPUT=L762-SIP4.2x10mers.unique.dedup.bam METRICS_FILE=L762-SIP4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L763-PUT3.2x10mers.unique.bam OUTPUT=L763-PUT3.2x10mers.unique.dedup.bam METRICS_FILE=L763-PUT3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L764-STP2.2x10mers.unique.bam OUTPUT=L764-STP2.2x10mers.unique.dedup.bam METRICS_FILE=L764-STP2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L765-GZF3.2x10mers.unique.bam OUTPUT=L765-GZF3.2x10mers.unique.dedup.bam METRICS_FILE=L765-GZF3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L766-BAS1.2x10mers.unique.bam OUTPUT=L766-BAS1.2x10mers.unique.dedup.bam METRICS_FILE=L766-BAS1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L767-SUT2.2x10mers.unique.bam OUTPUT=L767-SUT2.2x10mers.unique.dedup.bam METRICS_FILE=L767-SUT2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L768-ROX1.2x10mers.unique.bam OUTPUT=L768-ROX1.2x10mers.unique.dedup.bam METRICS_FILE=L768-ROX1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L769-LIF1.2x10mers.unique.bam OUTPUT=L769-LIF1.2x10mers.unique.dedup.bam METRICS_FILE=L769-LIF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L770-THO1.2x10mers.unique.bam OUTPUT=L770-THO1.2x10mers.unique.dedup.bam METRICS_FILE=L770-THO1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L771-HDA2.2x10mers.unique.bam OUTPUT=L771-HDA2.2x10mers.unique.dedup.bam METRICS_FILE=L771-HDA2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L772-NUP170.2x10mers.unique.bam OUTPUT=L772-NUP170.2x10mers.unique.dedup.bam METRICS_FILE=L772-NUP170.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L773-YPR015C.2x10mers.unique.bam OUTPUT=L773-YPR015C.2x10mers.unique.dedup.bam METRICS_FILE=L773-YPR015C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L774-SUB1.2x10mers.unique.bam OUTPUT=L774-SUB1.2x10mers.unique.dedup.bam METRICS_FILE=L774-SUB1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L775-IME1.2x10mers.unique.bam OUTPUT=L775-IME1.2x10mers.unique.dedup.bam METRICS_FILE=L775-IME1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L776-HIR1.2x10mers.unique.bam OUTPUT=L776-HIR1.2x10mers.unique.dedup.bam METRICS_FILE=L776-HIR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L777-MET32.2x10mers.unique.bam OUTPUT=L777-MET32.2x10mers.unique.dedup.bam METRICS_FILE=L777-MET32.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L778-RLM1.2x10mers.unique.bam OUTPUT=L778-RLM1.2x10mers.unique.dedup.bam METRICS_FILE=L778-RLM1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L779-YTA7.2x10mers.unique.bam OUTPUT=L779-YTA7.2x10mers.unique.dedup.bam METRICS_FILE=L779-YTA7.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L780-HIR2.2x10mers.unique.bam OUTPUT=L780-HIR2.2x10mers.unique.dedup.bam METRICS_FILE=L780-HIR2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L781-ZAP1.2x10mers.unique.bam OUTPUT=L781-ZAP1.2x10mers.unique.dedup.bam METRICS_FILE=L781-ZAP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L782-RDS1.2x10mers.unique.bam OUTPUT=L782-RDS1.2x10mers.unique.dedup.bam METRICS_FILE=L782-RDS1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L783-BDF1.2x10mers.unique.bam OUTPUT=L783-BDF1.2x10mers.unique.dedup.bam METRICS_FILE=L783-BDF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L784-HDA3.2x10mers.unique.bam OUTPUT=L784-HDA3.2x10mers.unique.dedup.bam METRICS_FILE=L784-HDA3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L785-CAD1.2x10mers.unique.bam OUTPUT=L785-CAD1.2x10mers.unique.dedup.bam METRICS_FILE=L785-CAD1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L786-SIR4.2x10mers.unique.bam OUTPUT=L786-SIR4.2x10mers.unique.dedup.bam METRICS_FILE=L786-SIR4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L787-REF2.2x10mers.unique.bam OUTPUT=L787-REF2.2x10mers.unique.dedup.bam METRICS_FILE=L787-REF2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L788-MET31.2x10mers.unique.bam OUTPUT=L788-MET31.2x10mers.unique.dedup.bam METRICS_FILE=L788-MET31.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L789-ARO80.2x10mers.unique.bam OUTPUT=L789-ARO80.2x10mers.unique.dedup.bam METRICS_FILE=L789-ARO80.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L790-RSF2.2x10mers.unique.bam OUTPUT=L790-RSF2.2x10mers.unique.dedup.bam METRICS_FILE=L790-RSF2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L791-CTF4.2x10mers.unique.bam OUTPUT=L791-CTF4.2x10mers.unique.dedup.bam METRICS_FILE=L791-CTF4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L792-CDC73.2x10mers.unique.bam OUTPUT=L792-CDC73.2x10mers.unique.dedup.bam METRICS_FILE=L792-CDC73.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L793-OAF1.2x10mers.unique.bam OUTPUT=L793-OAF1.2x10mers.unique.dedup.bam METRICS_FILE=L793-OAF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L794-UPC2.2x10mers.unique.bam OUTPUT=L794-UPC2.2x10mers.unique.dedup.bam METRICS_FILE=L794-UPC2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L795-MIG3.2x10mers.unique.bam OUTPUT=L795-MIG3.2x10mers.unique.dedup.bam METRICS_FILE=L795-MIG3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L796-UME6.2x10mers.unique.bam OUTPUT=L796-UME6.2x10mers.unique.dedup.bam METRICS_FILE=L796-UME6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L797-REI1.2x10mers.unique.bam OUTPUT=L797-REI1.2x10mers.unique.dedup.bam METRICS_FILE=L797-REI1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L798-YLR278C.2x10mers.unique.bam OUTPUT=L798-YLR278C.2x10mers.unique.dedup.bam METRICS_FILE=L798-YLR278C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L799-SFP1.2x10mers.unique.bam OUTPUT=L799-SFP1.2x10mers.unique.dedup.bam METRICS_FILE=L799-SFP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L800-ECM23.2x10mers.unique.bam OUTPUT=L800-ECM23.2x10mers.unique.dedup.bam METRICS_FILE=L800-ECM23.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L801-VHR1.2x10mers.unique.bam OUTPUT=L801-VHR1.2x10mers.unique.dedup.bam METRICS_FILE=L801-VHR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L802-DHH1.2x10mers.unique.bam OUTPUT=L802-DHH1.2x10mers.unique.dedup.bam METRICS_FILE=L802-DHH1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L803-YAP6.2x10mers.unique.bam OUTPUT=L803-YAP6.2x10mers.unique.dedup.bam METRICS_FILE=L803-YAP6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L804-GCN4.2x10mers.unique.bam OUTPUT=L804-GCN4.2x10mers.unique.dedup.bam METRICS_FILE=L804-GCN4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L805-PDR1.2x10mers.unique.bam OUTPUT=L805-PDR1.2x10mers.unique.dedup.bam METRICS_FILE=L805-PDR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L806-MIG2.2x10mers.unique.bam OUTPUT=L806-MIG2.2x10mers.unique.dedup.bam METRICS_FILE=L806-MIG2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L807-ADR1.2x10mers.unique.bam OUTPUT=L807-ADR1.2x10mers.unique.dedup.bam METRICS_FILE=L807-ADR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L808-YPR022C.2x10mers.unique.bam OUTPUT=L808-YPR022C.2x10mers.unique.dedup.bam METRICS_FILE=L808-YPR022C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L809-HAA1.2x10mers.unique.bam OUTPUT=L809-HAA1.2x10mers.unique.dedup.bam METRICS_FILE=L809-HAA1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L810-ARR1.2x10mers.unique.bam OUTPUT=L810-ARR1.2x10mers.unique.dedup.bam METRICS_FILE=L810-ARR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L811-YPR013C.2x10mers.unique.bam OUTPUT=L811-YPR013C.2x10mers.unique.dedup.bam METRICS_FILE=L811-YPR013C.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L812-RGT1.2x10mers.unique.bam OUTPUT=L812-RGT1.2x10mers.unique.dedup.bam METRICS_FILE=L812-RGT1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L813-RFX1.2x10mers.unique.bam OUTPUT=L813-RFX1.2x10mers.unique.dedup.bam METRICS_FILE=L813-RFX1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L814-IXR1.2x10mers.unique.bam OUTPUT=L814-IXR1.2x10mers.unique.dedup.bam METRICS_FILE=L814-IXR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L815-PDR8.2x10mers.unique.bam OUTPUT=L815-PDR8.2x10mers.unique.dedup.bam METRICS_FILE=L815-PDR8.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L816-ECM22.2x10mers.unique.bam OUTPUT=L816-ECM22.2x10mers.unique.dedup.bam METRICS_FILE=L816-ECM22.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L817-XRN1.2x10mers.unique.bam OUTPUT=L817-XRN1.2x10mers.unique.dedup.bam METRICS_FILE=L817-XRN1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L818-YRR1.2x10mers.unique.bam OUTPUT=L818-YRR1.2x10mers.unique.dedup.bam METRICS_FILE=L818-YRR1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L819-MSN2.2x10mers.unique.bam OUTPUT=L819-MSN2.2x10mers.unique.dedup.bam METRICS_FILE=L819-MSN2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L820-YPR196W.2x10mers.unique.bam OUTPUT=L820-YPR196W.2x10mers.unique.dedup.bam METRICS_FILE=L820-YPR196W.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L821-DAL81.2x10mers.unique.bam OUTPUT=L821-DAL81.2x10mers.unique.dedup.bam METRICS_FILE=L821-DAL81.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L822-HAT1.2x10mers.unique.bam OUTPUT=L822-HAT1.2x10mers.unique.dedup.bam METRICS_FILE=L822-HAT1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L823-PAF1.2x10mers.unique.bam OUTPUT=L823-PAF1.2x10mers.unique.dedup.bam METRICS_FILE=L823-PAF1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L824-NHP10.2x10mers.unique.bam OUTPUT=L824-NHP10.2x10mers.unique.dedup.bam METRICS_FILE=L824-NHP10.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L825-SPP1.2x10mers.unique.bam OUTPUT=L825-SPP1.2x10mers.unique.dedup.bam METRICS_FILE=L825-SPP1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L826-SFL1.2x10mers.unique.bam OUTPUT=L826-SFL1.2x10mers.unique.dedup.bam METRICS_FILE=L826-SFL1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L827-STP3.2x10mers.unique.bam OUTPUT=L827-STP3.2x10mers.unique.dedup.bam METRICS_FILE=L827-STP3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L828-YRM1.2x10mers.unique.bam OUTPUT=L828-YRM1.2x10mers.unique.dedup.bam METRICS_FILE=L828-YRM1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L829-ISW2.2x10mers.unique.bam OUTPUT=L829-ISW2.2x10mers.unique.dedup.bam METRICS_FILE=L829-ISW2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L830-HTZ1.2x10mers.unique.bam OUTPUT=L830-HTZ1.2x10mers.unique.dedup.bam METRICS_FILE=L830-HTZ1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L831-PHD1.2x10mers.unique.bam OUTPUT=L831-PHD1.2x10mers.unique.dedup.bam METRICS_FILE=L831-PHD1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L832-SWI5.2x10mers.unique.bam OUTPUT=L832-SWI5.2x10mers.unique.dedup.bam METRICS_FILE=L832-SWI5.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L833-ACA1.2x10mers.unique.bam OUTPUT=L833-ACA1.2x10mers.unique.dedup.bam METRICS_FILE=L833-ACA1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L834-INO2.2x10mers.unique.bam OUTPUT=L834-INO2.2x10mers.unique.dedup.bam METRICS_FILE=L834-INO2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L835-PHO4.2x10mers.unique.bam OUTPUT=L835-PHO4.2x10mers.unique.dedup.bam METRICS_FILE=L835-PHO4.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L836-MGA1.2x10mers.unique.bam OUTPUT=L836-MGA1.2x10mers.unique.dedup.bam METRICS_FILE=L836-MGA1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L837-MIG1.2x10mers.unique.bam OUTPUT=L837-MIG1.2x10mers.unique.dedup.bam METRICS_FILE=L837-MIG1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L838-HAP3.2x10mers.unique.bam OUTPUT=L838-HAP3.2x10mers.unique.dedup.bam METRICS_FILE=L838-HAP3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L839-YHR177W.2x10mers.unique.bam OUTPUT=L839-YHR177W.2x10mers.unique.dedup.bam METRICS_FILE=L839-YHR177W.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L847-GLN3.2x10mers.unique.bam OUTPUT=L847-GLN3.2x10mers.unique.dedup.bam METRICS_FILE=L847-GLN3.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L848-TOD6.2x10mers.unique.bam OUTPUT=L848-TOD6.2x10mers.unique.dedup.bam METRICS_FILE=L848-TOD6.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L925-MSN2-0min-rep1.2x10mers.unique.bam OUTPUT=L925-MSN2-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L925-MSN2-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L927-MSN1-0min-rep1.2x10mers.unique.bam OUTPUT=L927-MSN1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L927-MSN1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L928-HOG1-0min-rep1.2x10mers.unique.bam OUTPUT=L928-HOG1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L928-HOG1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L929-BDF1-0min-rep1.2x10mers.unique.bam OUTPUT=L929-BDF1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L929-BDF1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L930-YAP7-0min-rep1.2x10mers.unique.bam OUTPUT=L930-YAP7-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L930-YAP7-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L931-UME6-0min-rep1.2x10mers.unique.bam OUTPUT=L931-UME6-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L931-UME6-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L932-SMP1-0min-rep1.2x10mers.unique.bam OUTPUT=L932-SMP1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L932-SMP1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L933-YAP1-0min-rep1.2x10mers.unique.bam OUTPUT=L933-YAP1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L933-YAP1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L934-YAP3-0min-rep1.2x10mers.unique.bam OUTPUT=L934-YAP3-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L934-YAP3-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L935-ARR1-0min-rep1.2x10mers.unique.bam OUTPUT=L935-ARR1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L935-ARR1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L936-PHO4-0min-rep1.2x10mers.unique.bam OUTPUT=L936-PHO4-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L936-PHO4-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L937-YAP6-0min-rep1.2x10mers.unique.bam OUTPUT=L937-YAP6-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L937-YAP6-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L938-PDR3-0min-rep1.2x10mers.unique.bam OUTPUT=L938-PDR3-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L938-PDR3-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L939-GAT1-0min-rep1.2x10mers.unique.bam OUTPUT=L939-GAT1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L939-GAT1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L940-SKO1-0min-rep1.2x10mers.unique.bam OUTPUT=L940-SKO1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L940-SKO1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L941-CHA4-0min-rep1.2x10mers.unique.bam OUTPUT=L941-CHA4-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L941-CHA4-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L942-PHO2-0min-rep1.2x10mers.unique.bam OUTPUT=L942-PHO2-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L942-PHO2-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L943-ROX1-0min-rep1.2x10mers.unique.bam OUTPUT=L943-ROX1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L943-ROX1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L944-HOT1-0min-rep1.2x10mers.unique.bam OUTPUT=L944-HOT1-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L944-HOT1-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L945-YAP5-0min-rep1.2x10mers.unique.bam OUTPUT=L945-YAP5-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L945-YAP5-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L946-GAT4-0min-rep1.2x10mers.unique.bam OUTPUT=L946-GAT4-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L946-GAT4-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L947-SKN7-0min-rep1.2x10mers.unique.bam OUTPUT=L947-SKN7-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L947-SKN7-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L948-MSN4-0min-rep1.2x10mers.unique.bam OUTPUT=L948-MSN4-0min-rep1.2x10mers.unique.dedup.bam METRICS_FILE=L948-MSN4-0min-rep1.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L973-HOT1-0min-rep2.2x10mers.unique.bam OUTPUT=L973-HOT1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L973-HOT1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L974-ROX1-0min-rep2.2x10mers.unique.bam OUTPUT=L974-ROX1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L974-ROX1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L975-PHO2-0min-rep2.2x10mers.unique.bam OUTPUT=L975-PHO2-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L975-PHO2-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L976-CHA4-0min-rep2.2x10mers.unique.bam OUTPUT=L976-CHA4-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L976-CHA4-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L977-GAT4-0min-rep2.2x10mers.unique.bam OUTPUT=L977-GAT4-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L977-GAT4-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L978-YAP5-0min-rep2.2x10mers.unique.bam OUTPUT=L978-YAP5-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L978-YAP5-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L979-MSN2-0min-rep2.2x10mers.unique.bam OUTPUT=L979-MSN2-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L979-MSN2-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L980-BDF1-0min-rep2.2x10mers.unique.bam OUTPUT=L980-BDF1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L980-BDF1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L981-SFP1-0min-rep2.2x10mers.unique.bam OUTPUT=L981-SFP1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L981-SFP1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L982-SKN7-0min-rep2.2x10mers.unique.bam OUTPUT=L982-SKN7-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L982-SKN7-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L983-PDR3-0min-rep2.2x10mers.unique.bam OUTPUT=L983-PDR3-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L983-PDR3-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L984-HOG1-0min-rep2.2x10mers.unique.bam OUTPUT=L984-HOG1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L984-HOG1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L985-YAP3-0min-rep2.2x10mers.unique.bam OUTPUT=L985-YAP3-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L985-YAP3-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L986-MSN1-0min-rep2.2x10mers.unique.bam OUTPUT=L986-MSN1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L986-MSN1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L987-MSN4-0min-rep2.2x10mers.unique.bam OUTPUT=L987-MSN4-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L987-MSN4-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L988-YAP6-0min-rep2.2x10mers.unique.bam OUTPUT=L988-YAP6-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L988-YAP6-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L989-YAP1-0min-rep2.2x10mers.unique.bam OUTPUT=L989-YAP1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L989-YAP1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L990-SMP1-0min-rep2.2x10mers.unique.bam OUTPUT=L990-SMP1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L990-SMP1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L991-ARR1-0min-rep2.2x10mers.unique.bam OUTPUT=L991-ARR1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L991-ARR1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L992-UME6-0min-rep2.2x10mers.unique.bam OUTPUT=L992-UME6-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L992-UME6-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L993-PHO4-0min-rep2.2x10mers.unique.bam OUTPUT=L993-PHO4-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L993-PHO4-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L994-SKO1-0min-rep2.2x10mers.unique.bam OUTPUT=L994-SKO1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L994-SKO1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L995-YAP7-0min-rep2.2x10mers.unique.bam OUTPUT=L995-YAP7-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L995-YAP7-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L996-GAT1-0min-rep2.2x10mers.unique.bam OUTPUT=L996-GAT1-0min-rep2.2x10mers.unique.dedup.bam METRICS_FILE=L996-GAT1-0min-rep2.2x10mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &