module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Duroc_2W_1_Fat_ATAC-GSM4256374.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_1_Fat_ATAC-GSM4256374.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_1_Fat_ATAC-GSM4256374.2x36mers.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=Duroc_2W_2_Fat_ATAC-GSM4256375.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_2_Fat_ATAC-GSM4256375.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_2_Fat_ATAC-GSM4256375.2x36mers.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=Duroc_2W_1_Heart_ATAC-GSM4256376.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_1_Heart_ATAC-GSM4256376.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_1_Heart_ATAC-GSM4256376.2x36mers.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=Duroc_2W_2_Heart_ATAC-GSM4256377.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_2_Heart_ATAC-GSM4256377.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_2_Heart_ATAC-GSM4256377.2x36mers.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=Duroc_2W_1_Liver_ATAC-GSM4256378.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_1_Liver_ATAC-GSM4256378.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_1_Liver_ATAC-GSM4256378.2x36mers.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=Duroc_2W_2_Liver_ATAC-GSM4256379.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_2_Liver_ATAC-GSM4256379.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_2_Liver_ATAC-GSM4256379.2x36mers.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=Duroc_2W_1_Muscle_ATAC-GSM4256380.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_1_Muscle_ATAC-GSM4256380.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_1_Muscle_ATAC-GSM4256380.2x36mers.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=Duroc_2W_2_Muscle_ATAC-GSM4256381.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_2_Muscle_ATAC-GSM4256381.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_2_Muscle_ATAC-GSM4256381.2x36mers.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=Duroc_2W_1_Spleen_ATAC-GSM4256382.2x36mers.noMT.unique.bam OUTPUT=Duroc_2W_1_Spleen_ATAC-GSM4256382.2x36mers.noMT.unique.dedup.bam METRICS_FILE=Duroc_2W_1_Spleen_ATAC-GSM4256382.2x36mers.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=ES_2W_1_Fat_ATAC-GSM4256383.2x36mers.noMT.unique.bam OUTPUT=ES_2W_1_Fat_ATAC-GSM4256383.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_1_Fat_ATAC-GSM4256383.2x36mers.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=ES_2W_2_Fat_ATAC-GSM4256384.2x36mers.noMT.unique.bam OUTPUT=ES_2W_2_Fat_ATAC-GSM4256384.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_2_Fat_ATAC-GSM4256384.2x36mers.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=ES_2W_1_Heart_ATAC-GSM4256385.2x36mers.noMT.unique.bam OUTPUT=ES_2W_1_Heart_ATAC-GSM4256385.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_1_Heart_ATAC-GSM4256385.2x36mers.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=ES_2W_2_Liver_ATAC-GSM4256387.2x36mers.noMT.unique.bam OUTPUT=ES_2W_2_Liver_ATAC-GSM4256387.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_2_Liver_ATAC-GSM4256387.2x36mers.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=ES_2W_1_Muscle_ATAC-GSM4256388.2x36mers.noMT.unique.bam OUTPUT=ES_2W_1_Muscle_ATAC-GSM4256388.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_1_Muscle_ATAC-GSM4256388.2x36mers.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=ES_2W_2_Muscle_ATAC-GSM4256389.2x36mers.noMT.unique.bam OUTPUT=ES_2W_2_Muscle_ATAC-GSM4256389.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_2_Muscle_ATAC-GSM4256389.2x36mers.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=ES_2W_1_Spleen_ATAC-GSM4256390.2x36mers.noMT.unique.bam OUTPUT=ES_2W_1_Spleen_ATAC-GSM4256390.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ES_2W_1_Spleen_ATAC-GSM4256390.2x36mers.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=LW_2W_1_Fat_ATAC-GSM4256391.2x36mers.noMT.unique.bam OUTPUT=LW_2W_1_Fat_ATAC-GSM4256391.2x36mers.noMT.unique.dedup.bam METRICS_FILE=LW_2W_1_Fat_ATAC-GSM4256391.2x36mers.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=LW_2W_2_Fat_ATAC-GSM4256392.2x36mers.noMT.unique.bam OUTPUT=LW_2W_2_Fat_ATAC-GSM4256392.2x36mers.noMT.unique.dedup.bam METRICS_FILE=LW_2W_2_Fat_ATAC-GSM4256392.2x36mers.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=LW_2W_1_Liver_ATAC-GSM4256393.2x36mers.noMT.unique.bam OUTPUT=LW_2W_1_Liver_ATAC-GSM4256393.2x36mers.noMT.unique.dedup.bam METRICS_FILE=LW_2W_1_Liver_ATAC-GSM4256393.2x36mers.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=LW_2W_1_Muscle_ATAC-GSM4256395.2x36mers.noMT.unique.bam OUTPUT=LW_2W_1_Muscle_ATAC-GSM4256395.2x36mers.noMT.unique.dedup.bam METRICS_FILE=LW_2W_1_Muscle_ATAC-GSM4256395.2x36mers.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=LW_2W_2_Muscle_ATAC-GSM4256396.2x36mers.noMT.unique.bam OUTPUT=LW_2W_2_Muscle_ATAC-GSM4256396.2x36mers.noMT.unique.dedup.bam METRICS_FILE=LW_2W_2_Muscle_ATAC-GSM4256396.2x36mers.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=MS_2W_1_Fat_ATAC-GSM4256397.2x36mers.noMT.unique.bam OUTPUT=MS_2W_1_Fat_ATAC-GSM4256397.2x36mers.noMT.unique.dedup.bam METRICS_FILE=MS_2W_1_Fat_ATAC-GSM4256397.2x36mers.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=MS_2W_2_Fat_ATAC-GSM4256398.2x36mers.noMT.unique.bam OUTPUT=MS_2W_2_Fat_ATAC-GSM4256398.2x36mers.noMT.unique.dedup.bam METRICS_FILE=MS_2W_2_Fat_ATAC-GSM4256398.2x36mers.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=MS_2W_2_Liver_ATAC-GSM4256400.2x36mers.noMT.unique.bam OUTPUT=MS_2W_2_Liver_ATAC-GSM4256400.2x36mers.noMT.unique.dedup.bam METRICS_FILE=MS_2W_2_Liver_ATAC-GSM4256400.2x36mers.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=MS_2W_2_Muscle_ATAC-GSM4256401.2x36mers.noMT.unique.bam OUTPUT=MS_2W_2_Muscle_ATAC-GSM4256401.2x36mers.noMT.unique.dedup.bam METRICS_FILE=MS_2W_2_Muscle_ATAC-GSM4256401.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &