module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.hg19-male.nochrM.bam OUTPUT=2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.hg19-male.nochrM.dedup.bam METRICS_FILE=2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.hg19-male.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true