module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3468-lung_firboblasts_HCMV.hg38-male.2x36mers.unique.bam OUTPUT=L3468-lung_firboblasts_HCMV.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3468-lung_firboblasts_HCMV.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3468-lung_firboblasts_HCMV.merlin.2x36mers.unique.bam OUTPUT=L3468-lung_firboblasts_HCMV.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3468-lung_firboblasts_HCMV.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3470-hEC-2.hg38-male.2x36mers.unique.bam OUTPUT=L3470-hEC-2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3470-hEC-2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3471-hEC-3.hg38-male.2x36mers.unique.bam OUTPUT=L3471-hEC-3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3471-hEC-3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3472-hInv-1.hg38-male.2x36mers.unique.bam OUTPUT=L3472-hInv-1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3472-hInv-1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3474-hInv-1.hg38-male.2x36mers.unique.bam OUTPUT=L3474-hInv-1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3474-hInv-1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3476-hECPos-2.hg38-male.2x36mers.unique.bam OUTPUT=L3476-hECPos-2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3476-hECPos-2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3477-hECPos-3.hg38-male.2x36mers.unique.bam OUTPUT=L3477-hECPos-3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3477-hECPos-3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3479-hInvPos-2.hg38-male.2x36mers.unique.bam OUTPUT=L3479-hInvPos-2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3479-hInvPos-2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3480-hInvPos-3.hg38-male.2x36mers.unique.bam OUTPUT=L3480-hInvPos-3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3480-hInvPos-3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3481-CRE-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3481-CRE-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3481-CRE-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3482-CRE-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3482-CRE-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3482-CRE-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3483-noCRE-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3483-noCRE-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3483-noCRE-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3484-noCRE-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3484-noCRE-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3484-noCRE-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3485-EC-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3485-EC-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3485-EC-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3486-EC-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3486-EC-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3486-EC-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3489-hInv-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3489-hInv-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3489-hInv-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3493-Hanbang_WT_NRSF.hg38-male.2x36mers.unique.bam OUTPUT=L3493-Hanbang_WT_NRSF.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3493-Hanbang_WT_NRSF.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3494-Hanbang_HS_NRSF.hg38-male.2x36mers.unique.bam OUTPUT=L3494-Hanbang_HS_NRSF.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3494-Hanbang_HS_NRSF.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3495-Hanbang_AS_NRSF.hg38-male.2x36mers.unique.bam OUTPUT=L3495-Hanbang_AS_NRSF.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3495-Hanbang_AS_NRSF.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3496-lung_firboblasts_H3K27me3.hg38-male.2x36mers.unique.bam OUTPUT=L3496-lung_firboblasts_H3K27me3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3496-lung_firboblasts_H3K27me3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3496-lung_firboblasts_H3K27me3.merlin.2x36mers.unique.bam OUTPUT=L3496-lung_firboblasts_H3K27me3.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3496-lung_firboblasts_H3K27me3.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3497-lung_firboblasts_CTCF.hg38-male.2x36mers.unique.bam OUTPUT=L3497-lung_firboblasts_CTCF.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3497-lung_firboblasts_CTCF.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3497-lung_firboblasts_CTCF.merlin.2x36mers.unique.bam OUTPUT=L3497-lung_firboblasts_CTCF.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3497-lung_firboblasts_CTCF.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3498-lung_firboblasts_H3K4me3.hg38-male.2x36mers.unique.bam OUTPUT=L3498-lung_firboblasts_H3K4me3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3498-lung_firboblasts_H3K4me3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3498-lung_firboblasts_H3K4me3.merlin.2x36mers.unique.bam OUTPUT=L3498-lung_firboblasts_H3K4me3.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3498-lung_firboblasts_H3K4me3.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3499-lung_firboblasts_4H8.hg38-male.2x36mers.unique.bam OUTPUT=L3499-lung_firboblasts_4H8.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3499-lung_firboblasts_4H8.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3499-lung_firboblasts_4H8.merlin.2x36mers.unique.bam OUTPUT=L3499-lung_firboblasts_4H8.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3499-lung_firboblasts_4H8.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3500-lung_firboblasts_H3K27ac.hg38-male.2x36mers.unique.bam OUTPUT=L3500-lung_firboblasts_H3K27ac.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3500-lung_firboblasts_H3K27ac.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3500-lung_firboblasts_H3K27ac.merlin.2x36mers.unique.bam OUTPUT=L3500-lung_firboblasts_H3K27ac.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3500-lung_firboblasts_H3K27ac.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3501-lung_firboblasts_H3K9me3.hg38-male.2x36mers.unique.bam OUTPUT=L3501-lung_firboblasts_H3K9me3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3501-lung_firboblasts_H3K9me3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3501-lung_firboblasts_H3K9me3.merlin.2x36mers.unique.bam OUTPUT=L3501-lung_firboblasts_H3K9me3.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3501-lung_firboblasts_H3K9me3.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3502-lung_firboblasts_H3K4me1.hg38-male.2x36mers.unique.bam OUTPUT=L3502-lung_firboblasts_H3K4me1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3502-lung_firboblasts_H3K4me1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3502-lung_firboblasts_H3K4me1.merlin.2x36mers.unique.bam OUTPUT=L3502-lung_firboblasts_H3K4me1.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3502-lung_firboblasts_H3K4me1.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3503-Hanbang_WT_input.hg38-male.2x36mers.unique.bam OUTPUT=L3503-Hanbang_WT_input.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3503-Hanbang_WT_input.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3504-Hanbang_HS_input.hg38-male.2x36mers.unique.bam OUTPUT=L3504-Hanbang_HS_input.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3504-Hanbang_HS_input.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3505-Hanbang_AS_input.hg38-male.2x36mers.unique.bam OUTPUT=L3505-Hanbang_AS_input.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3505-Hanbang_AS_input.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3506-lung_firboblasts_HCMV-Input.hg38-male.2x36mers.unique.bam OUTPUT=L3506-lung_firboblasts_HCMV-Input.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3506-lung_firboblasts_HCMV-Input.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3506-lung_firboblasts_HCMV-Input.merlin.2x36mers.unique.bam OUTPUT=L3506-lung_firboblasts_HCMV-Input.merlin.2x36mers.unique.dedup.bam METRICS_FILE=L3506-lung_firboblasts_HCMV-Input.merlin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3507-CRE-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3507-CRE-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3507-CRE-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3508-CRE-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3508-CRE-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3508-CRE-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3509-CRE-rep3.hg38-male.2x36mers.unique.bam OUTPUT=L3509-CRE-rep3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3509-CRE-rep3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3510-noCRE-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3510-noCRE-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3510-noCRE-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3511-noCRE-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3511-noCRE-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3511-noCRE-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3512-noCRE-rep3.hg38-male.2x36mers.unique.bam OUTPUT=L3512-noCRE-rep3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3512-noCRE-rep3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3513-EC-rep1.hg38-male.2x36mers.unique.bam OUTPUT=L3513-EC-rep1.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3513-EC-rep1.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3514-EC-rep2.hg38-male.2x36mers.unique.bam OUTPUT=L3514-EC-rep2.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3514-EC-rep2.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L3515-EC-rep3.hg38-male.2x36mers.unique.bam OUTPUT=L3515-EC-rep3.hg38-male.2x36mers.unique.dedup.bam METRICS_FILE=L3515-EC-rep3.hg38-male.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true