module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=ATAC-seq_K562_Control-rep1-GSM2695560.36mers.unique.bam OUTPUT=ATAC-seq_K562_Control-rep1-GSM2695560.36mers.unique.dedup.bam METRICS_FILE=ATAC-seq_K562_Control-rep1-GSM2695560.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=ATAC-seq_K562_Control-rep2-GSM2695561.36mers.unique.bam OUTPUT=ATAC-seq_K562_Control-rep2-GSM2695561.36mers.unique.dedup.bam METRICS_FILE=ATAC-seq_K562_Control-rep2-GSM2695561.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=ATAC-seq_K562_Control-rep3-GSM2695562.36mers.unique.bam OUTPUT=ATAC-seq_K562_Control-rep3-GSM2695562.36mers.unique.dedup.bam METRICS_FILE=ATAC-seq_K562_Control-rep3-GSM2695562.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true