module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.2x36mers.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=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.2x36mers.noMT.unique.bam OUTPUT=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.2x36mers.noMT.unique.dedup.bam METRICS_FILE=ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.2x36mers.noMT.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &