module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=K562-Oct4-Snyder-Rep1-ENCFF002EEQ.36mers.unique.bam OUTPUT=K562-Oct4-Snyder-Rep1-ENCFF002EEQ.36mers.unique.dedup.bam METRICS_FILE=K562-Oct4-Snyder-Rep1-ENCFF002EEQ.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=K562-Oct4-Snyder-Rep1-ENCFF002EEN.36mers.unique.bam OUTPUT=K562-Oct4-Snyder-Rep1-ENCFF002EEN.36mers.unique.dedup.bam METRICS_FILE=K562-Oct4-Snyder-Rep1-ENCFF002EEN.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=K562-Control-Snyder-Rep1-ENCFF002ECW.36mers.unique.bam OUTPUT=K562-Control-Snyder-Rep1-ENCFF002ECW.36mers.unique.dedup.bam METRICS_FILE=K562-Control-Snyder-Rep1-ENCFF002ECW.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=K562-Control-Snyder-Rep1-ENCFF002ECS.36mers.unique.bam OUTPUT=K562-Control-Snyder-Rep1-ENCFF002ECS.36mers.unique.dedup.bam METRICS_FILE=K562-Control-Snyder-Rep1-ENCFF002ECS.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GM23338-Oct4-HAIB-Rep1-ENCFF647APA.36mers.unique.bam OUTPUT=GM23338-Oct4-HAIB-Rep1-ENCFF647APA.36mers.unique.dedup.bam METRICS_FILE=GM23338-Oct4-HAIB-Rep1-ENCFF647APA.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GM23338-Oct4-HAIB-Rep2-ENCFF986KEK.36mers.unique.bam OUTPUT=GM23338-Oct4-HAIB-Rep2-ENCFF986KEK.36mers.unique.dedup.bam METRICS_FILE=GM23338-Oct4-HAIB-Rep2-ENCFF986KEK.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GM23338-Control-HAIB-Rep1-ENCFF484RXR.36mers.unique.bam OUTPUT=GM23338-Control-HAIB-Rep1-ENCFF484RXR.36mers.unique.dedup.bam METRICS_FILE=GM23338-Control-HAIB-Rep1-ENCFF484RXR.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GM23338-Control-HAIB-Rep2-ENCFF252PYF.36mers.unique.bam OUTPUT=GM23338-Control-HAIB-Rep2-ENCFF252PYF.36mers.unique.dedup.bam METRICS_FILE=GM23338-Control-HAIB-Rep2-ENCFF252PYF.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=H1-hESC-Oct4-HAIB-Rep1-ENCFF000ORV.36mers.unique.bam OUTPUT=H1-hESC-Oct4-HAIB-Rep1-ENCFF000ORV.36mers.unique.dedup.bam METRICS_FILE=H1-hESC-Oct4-HAIB-Rep1-ENCFF000ORV.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=H1-hESC-Oct4-HAIB-Rep2-ENCFF000ORW.36mers.unique.bam OUTPUT=H1-hESC-Oct4-HAIB-Rep2-ENCFF000ORW.36mers.unique.dedup.bam METRICS_FILE=H1-hESC-Oct4-HAIB-Rep2-ENCFF000ORW.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=H1-hESC-Control-HAIB-Rep0-ENCFF000OSP.36mers.unique.bam OUTPUT=H1-hESC-Control-HAIB-Rep0-ENCFF000OSP.36mers.unique.dedup.bam METRICS_FILE=H1-hESC-Control-HAIB-Rep0-ENCFF000OSP.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=H1-hESC-Control-HAIB-Rep1-ENCFF000OST.36mers.unique.bam OUTPUT=H1-hESC-Control-HAIB-Rep1-ENCFF000OST.36mers.unique.dedup.bam METRICS_FILE=H1-hESC-Control-HAIB-Rep1-ENCFF000OST.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=H1-hESC-Control-HAIB-Rep2-ENCFF000OSS.36mers.unique.bam OUTPUT=H1-hESC-Control-HAIB-Rep2-ENCFF000OSS.36mers.unique.dedup.bam METRICS_FILE=H1-hESC-Control-HAIB-Rep2-ENCFF000OSS.36mers.unique.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true