module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel; module load java; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true