module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Heart-0day-rep1-ATAC-GSM7164788.2x36mers.noMT.unique.bam OUTPUT=Heart-0day-rep1-ATAC-GSM7164788.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Heart-0day-rep1-ATAC-GSM7164788.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Heart-0day-rep2-ATAC-GSM7164789.2x36mers.noMT.unique.bam OUTPUT=Heart-0day-rep2-ATAC-GSM7164789.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Heart-0day-rep2-ATAC-GSM7164789.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Kidney-0day-rep1-ATAC-GSM7164790.2x36mers.noMT.unique.bam OUTPUT=Kidney-0day-rep1-ATAC-GSM7164790.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Kidney-0day-rep1-ATAC-GSM7164790.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Kidney-0day-rep2-ATAC-GSM7164791.2x36mers.noMT.unique.bam OUTPUT=Kidney-0day-rep2-ATAC-GSM7164791.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Kidney-0day-rep2-ATAC-GSM7164791.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Lung-0day-rep1-ATAC-GSM7164792.2x36mers.noMT.unique.bam OUTPUT=Lung-0day-rep1-ATAC-GSM7164792.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Lung-0day-rep1-ATAC-GSM7164792.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Lung-0day-rep2-ATAC-GSM7164793.2x36mers.noMT.unique.bam OUTPUT=Lung-0day-rep2-ATAC-GSM7164793.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Lung-0day-rep2-ATAC-GSM7164793.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Muscle-0day-rep1-ATAC-GSM7164794.2x36mers.noMT.unique.bam OUTPUT=Muscle-0day-rep1-ATAC-GSM7164794.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Muscle-0day-rep1-ATAC-GSM7164794.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Muscle-0day-rep2-ATAC-GSM7164795.2x36mers.noMT.unique.bam OUTPUT=Muscle-0day-rep2-ATAC-GSM7164795.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Muscle-0day-rep2-ATAC-GSM7164795.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Spleen-0day-rep1-ATAC-GSM7164796.2x36mers.noMT.unique.bam OUTPUT=Spleen-0day-rep1-ATAC-GSM7164796.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Spleen-0day-rep1-ATAC-GSM7164796.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Spleen-0day-rep2-ATAC-GSM7164797.2x36mers.noMT.unique.bam OUTPUT=Spleen-0day-rep2-ATAC-GSM7164797.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Spleen-0day-rep2-ATAC-GSM7164797.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-0day-rep1-ATAC-GSM7164798.2x36mers.noMT.unique.bam OUTPUT=Liver-0day-rep1-ATAC-GSM7164798.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-0day-rep1-ATAC-GSM7164798.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-0day-rep2-ATAC-GSM7164799.2x36mers.noMT.unique.bam OUTPUT=Liver-0day-rep2-ATAC-GSM7164799.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-0day-rep2-ATAC-GSM7164799.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-28day-rep1-ATAC-GSM7164800.2x36mers.noMT.unique.bam OUTPUT=Liver-28day-rep1-ATAC-GSM7164800.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-28day-rep1-ATAC-GSM7164800.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-28day-rep2-ATAC-GSM7164801.2x36mers.noMT.unique.bam OUTPUT=Liver-28day-rep2-ATAC-GSM7164801.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-28day-rep2-ATAC-GSM7164801.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-180day-rep1-ATAC-GSM7164802.2x36mers.noMT.unique.bam OUTPUT=Liver-180day-rep1-ATAC-GSM7164802.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-180day-rep1-ATAC-GSM7164802.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Liver-180day-rep2-ATAC-GSM7164803.2x36mers.noMT.unique.bam OUTPUT=Liver-180day-rep2-ATAC-GSM7164803.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Liver-180day-rep2-ATAC-GSM7164803.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &