module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Br2-CRR994956.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Br2-CRR994956.2x36mers.noMT.bwa.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=DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Br3-CRR994957.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Br3-CRR994957.2x36mers.noMT.bwa.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=DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Li2-CRR994959.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Li2-CRR994959.2x36mers.noMT.bwa.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=DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Li3-CRR994960.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Li3-CRR994960.2x36mers.noMT.bwa.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=DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Mu1-CRR994961.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Mu1-CRR994961.2x36mers.noMT.bwa.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=DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Mu2-CRR994962.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Mu2-CRR994962.2x36mers.noMT.bwa.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=DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.bam OUTPUT=DB115_Mu3-CRR994963.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB115_Mu3-CRR994963.2x36mers.noMT.bwa.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=DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_E_Br1-CRR994964.2x36mers.noMT.bwa.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=DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_E_Li1-CRR994965.2x36mers.noMT.bwa.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=DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_I_Br2-CRR994967.2x36mers.noMT.bwa.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=DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_I_Li2-CRR994968.2x36mers.noMT.bwa.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=DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_I_Mu2-CRR994969.2x36mers.noMT.bwa.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=DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_J_Br3-CRR994970.2x36mers.noMT.bwa.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=DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_J_Li3-CRR994971.2x36mers.noMT.bwa.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=DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.bam OUTPUT=DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB168_J_Mu3-CRR994972.2x36mers.noMT.bwa.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=DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Br1-CRR994973.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Br1-CRR994973.2x36mers.noMT.bwa.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=DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Li1-CRR994976.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Li1-CRR994976.2x36mers.noMT.bwa.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=DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Li2-CRR994977.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Li2-CRR994977.2x36mers.noMT.bwa.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=DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Li3-CRR994978.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Li3-CRR994978.2x36mers.noMT.bwa.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=DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Mu1-CRR994979.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Mu1-CRR994979.2x36mers.noMT.bwa.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=DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Mu2-CRR994980.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Mu2-CRR994980.2x36mers.noMT.bwa.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=DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Mu3-CRR994981.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Mu3-CRR994981.2x36mers.noMT.bwa.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=DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Pl1-CRR994982.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Pl1-CRR994982.2x36mers.noMT.bwa.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=DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Pl2-CRR994983.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Pl2-CRR994983.2x36mers.noMT.bwa.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=DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.bam OUTPUT=DB40_Pl3-CRR994984.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB40_Pl3-CRR994984.2x36mers.noMT.bwa.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=DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Br1-CRR994985.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Br1-CRR994985.2x36mers.noMT.bwa.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=DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Br3-CRR994987.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Br3-CRR994987.2x36mers.noMT.bwa.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=DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Li2-CRR994989.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Li2-CRR994989.2x36mers.noMT.bwa.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=DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Li3-CRR994990.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Li3-CRR994990.2x36mers.noMT.bwa.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=DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Mu1-CRR994991.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Mu1-CRR994991.2x36mers.noMT.bwa.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=DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Mu2-CRR994992.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Mu2-CRR994992.2x36mers.noMT.bwa.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=DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Mu3-CRR994993.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Mu3-CRR994993.2x36mers.noMT.bwa.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=DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.bam OUTPUT=DB70_Pl1-CRR994994.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DB70_Pl1-CRR994994.2x36mers.noMT.bwa.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=DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Br1-CRR994995.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Br1-CRR994995.2x36mers.noMT.bwa.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=DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Br2-CRR994996.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Br2-CRR994996.2x36mers.noMT.bwa.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=DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Br3-CRR994997.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Br3-CRR994997.2x36mers.noMT.bwa.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=DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Li1-CRR994998.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Li1-CRR994998.2x36mers.noMT.bwa.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=DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Li2-CRR994999.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Li2-CRR994999.2x36mers.noMT.bwa.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=DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Li3-CRR995000.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Li3-CRR995000.2x36mers.noMT.bwa.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=DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Mu1-CRR995001.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Mu1-CRR995001.2x36mers.noMT.bwa.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=DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Mu2-CRR995002.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Mu2-CRR995002.2x36mers.noMT.bwa.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=DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.bam OUTPUT=DS115_Mu3-CRR995003.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS115_Mu3-CRR995003.2x36mers.noMT.bwa.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=DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_M_Br1-CRR995004.2x36mers.noMT.bwa.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=DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_M_Li1-CRR995005.2x36mers.noMT.bwa.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=DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_N_Br2-CRR995007.2x36mers.noMT.bwa.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=DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_N_Li2-CRR995008.2x36mers.noMT.bwa.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=DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_N_Mu2-CRR995009.2x36mers.noMT.bwa.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=DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_O_Br3-CRR995010.2x36mers.noMT.bwa.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=DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.bam OUTPUT=DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS168_O_Li3-CRR995011.2x36mers.noMT.bwa.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=DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Br1-CRR995013.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Br1-CRR995013.2x36mers.noMT.bwa.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=DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Br2-CRR995014.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Br2-CRR995014.2x36mers.noMT.bwa.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=DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Br3-CRR995015.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Br3-CRR995015.2x36mers.noMT.bwa.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=DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Li2-CRR995016.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Li2-CRR995016.2x36mers.noMT.bwa.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=DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Li3-CRR995017.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Li3-CRR995017.2x36mers.noMT.bwa.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=DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Mu1-CRR995018.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Mu1-CRR995018.2x36mers.noMT.bwa.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=DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Mu2-CRR995019.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Mu2-CRR995019.2x36mers.noMT.bwa.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=DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Mu3-CRR995020.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Mu3-CRR995020.2x36mers.noMT.bwa.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=DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Pl1-CRR995021.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Pl1-CRR995021.2x36mers.noMT.bwa.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=DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Pl2-CRR995022.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Pl2-CRR995022.2x36mers.noMT.bwa.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=DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.bam OUTPUT=DS40_Pl3-CRR995023.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS40_Pl3-CRR995023.2x36mers.noMT.bwa.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=DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Br1-CRR995024.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Br1-CRR995024.2x36mers.noMT.bwa.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=DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Br2-CRR995025.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Br2-CRR995025.2x36mers.noMT.bwa.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=DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Br3-CRR995026.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Br3-CRR995026.2x36mers.noMT.bwa.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=DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Li1-CRR995027.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Li1-CRR995027.2x36mers.noMT.bwa.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=DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Li2-CRR995028.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Li2-CRR995028.2x36mers.noMT.bwa.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=DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Li3-CRR995029.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Li3-CRR995029.2x36mers.noMT.bwa.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=DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Mu1-CRR995030.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Mu1-CRR995030.2x36mers.noMT.bwa.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=DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Mu2-CRR995031.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Mu2-CRR995031.2x36mers.noMT.bwa.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=DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Mu3-CRR995032.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Mu3-CRR995032.2x36mers.noMT.bwa.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=DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Pl1-CRR995033.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Pl1-CRR995033.2x36mers.noMT.bwa.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=DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.bam OUTPUT=DS70_Pl3-CRR995034.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=DS70_Pl3-CRR995034.2x36mers.noMT.bwa.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=LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Br1-CRR995035.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Br1-CRR995035.2x36mers.noMT.bwa.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=LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Br2-CRR995036.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Br2-CRR995036.2x36mers.noMT.bwa.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=LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Br3-CRR995037.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Br3-CRR995037.2x36mers.noMT.bwa.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=LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Li1-CRR995038.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Li1-CRR995038.2x36mers.noMT.bwa.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=LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Li2-CRR995039.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Li2-CRR995039.2x36mers.noMT.bwa.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=LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Li3-CRR995040.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Li3-CRR995040.2x36mers.noMT.bwa.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=LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Mu1-CRR995041.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Mu1-CRR995041.2x36mers.noMT.bwa.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=LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Mu2-CRR995042.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Mu2-CRR995042.2x36mers.noMT.bwa.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=LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.bam OUTPUT=LB115_Mu3-CRR995043.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB115_Mu3-CRR995043.2x36mers.noMT.bwa.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=LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_F_Br2-CRR995044.2x36mers.noMT.bwa.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=LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_F_Li2-CRR995045.2x36mers.noMT.bwa.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=LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_F_Mu2-CRR995046.2x36mers.noMT.bwa.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=LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_G_Br1-CRR995047.2x36mers.noMT.bwa.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=LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_G_Li1-CRR995048.2x36mers.noMT.bwa.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=LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_G_Mu1-CRR995049.2x36mers.noMT.bwa.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=LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_H_Br3-CRR995050.2x36mers.noMT.bwa.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=LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_H_Li3-CRR995051.2x36mers.noMT.bwa.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=LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.bam OUTPUT=LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB168_H_Mu3-CRR995052.2x36mers.noMT.bwa.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=LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Br1-CRR995053.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Br1-CRR995053.2x36mers.noMT.bwa.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=LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Br3-CRR995055.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Br3-CRR995055.2x36mers.noMT.bwa.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=LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Li1-CRR995056.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Li1-CRR995056.2x36mers.noMT.bwa.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=LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Li2-CRR995057.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Li2-CRR995057.2x36mers.noMT.bwa.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=LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Li3-CRR995058.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Li3-CRR995058.2x36mers.noMT.bwa.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=LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Mu2-CRR995060.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Mu2-CRR995060.2x36mers.noMT.bwa.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=LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Mu3-CRR995061.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Mu3-CRR995061.2x36mers.noMT.bwa.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=LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Pl1-CRR995062.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Pl1-CRR995062.2x36mers.noMT.bwa.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=LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Pl2-CRR995063.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Pl2-CRR995063.2x36mers.noMT.bwa.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=LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.bam OUTPUT=LB40_Pl3-CRR995064.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB40_Pl3-CRR995064.2x36mers.noMT.bwa.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=LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Br1-CRR995065.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Br1-CRR995065.2x36mers.noMT.bwa.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=LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Br2-CRR995066.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Br2-CRR995066.2x36mers.noMT.bwa.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=LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Br3-CRR995067.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Br3-CRR995067.2x36mers.noMT.bwa.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=LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Li1-CRR995068.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Li1-CRR995068.2x36mers.noMT.bwa.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=LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Li2-CRR995069.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Li2-CRR995069.2x36mers.noMT.bwa.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=LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Li3-CRR995070.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Li3-CRR995070.2x36mers.noMT.bwa.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=LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Mu1-CRR995071.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Mu1-CRR995071.2x36mers.noMT.bwa.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=LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Mu2-CRR995072.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Mu2-CRR995072.2x36mers.noMT.bwa.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=LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Mu3-CRR995073.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Mu3-CRR995073.2x36mers.noMT.bwa.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=LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Pl1-CRR995074.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Pl1-CRR995074.2x36mers.noMT.bwa.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=LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Pl2-CRR995075.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Pl2-CRR995075.2x36mers.noMT.bwa.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=LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.bam OUTPUT=LB70_Pl3-CRR995076.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LB70_Pl3-CRR995076.2x36mers.noMT.bwa.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=LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Br1-CRR995077.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Br1-CRR995077.2x36mers.noMT.bwa.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=LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Br2-CRR995078.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Br2-CRR995078.2x36mers.noMT.bwa.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=LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Br3-CRR995079.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Br3-CRR995079.2x36mers.noMT.bwa.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=LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Li1-CRR995080.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Li1-CRR995080.2x36mers.noMT.bwa.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=LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Li2-CRR995081.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Li2-CRR995081.2x36mers.noMT.bwa.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=LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Li3-CRR995082.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Li3-CRR995082.2x36mers.noMT.bwa.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=LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Mu1-CRR995083.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Mu1-CRR995083.2x36mers.noMT.bwa.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=LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Mu2-CRR995084.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Mu2-CRR995084.2x36mers.noMT.bwa.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=LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.bam OUTPUT=LS115_Mu3-CRR995085.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS115_Mu3-CRR995085.2x36mers.noMT.bwa.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=LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_B_Li1-CRR995087.2x36mers.noMT.bwa.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=LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_B_Mu1-CRR995088.2x36mers.noMT.bwa.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=LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_C_Br2-CRR995089.2x36mers.noMT.bwa.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=LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_C_Li2-CRR995090.2x36mers.noMT.bwa.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=LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_C_Mu2-CRR995091.2x36mers.noMT.bwa.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=LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.bam OUTPUT=LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS168_L_Li3-CRR995092.2x36mers.noMT.bwa.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=LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Br2-CRR995095.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Br2-CRR995095.2x36mers.noMT.bwa.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=LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Br3-CRR995096.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Br3-CRR995096.2x36mers.noMT.bwa.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=LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Li1-CRR995097.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Li1-CRR995097.2x36mers.noMT.bwa.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=LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Li2-CRR995098.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Li2-CRR995098.2x36mers.noMT.bwa.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=LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Li3-CRR995099.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Li3-CRR995099.2x36mers.noMT.bwa.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=LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Mu1-CRR995100.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Mu1-CRR995100.2x36mers.noMT.bwa.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=LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Mu2-CRR995101.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Mu2-CRR995101.2x36mers.noMT.bwa.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=LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Mu3-CRR995102.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Mu3-CRR995102.2x36mers.noMT.bwa.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=LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Pl1-CRR995103.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Pl1-CRR995103.2x36mers.noMT.bwa.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=LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Pl2-CRR995104.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Pl2-CRR995104.2x36mers.noMT.bwa.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=LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.bam OUTPUT=LS40_Pl3-CRR995105.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS40_Pl3-CRR995105.2x36mers.noMT.bwa.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=LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Br1-CRR995106.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Br1-CRR995106.2x36mers.noMT.bwa.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=LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Br2-CRR995107.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Br2-CRR995107.2x36mers.noMT.bwa.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=LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Br3-CRR995108.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Br3-CRR995108.2x36mers.noMT.bwa.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=LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Li1-CRR995109.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Li1-CRR995109.2x36mers.noMT.bwa.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=LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Li2-CRR995110.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Li2-CRR995110.2x36mers.noMT.bwa.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=LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Li3-CRR995111.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Li3-CRR995111.2x36mers.noMT.bwa.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=LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Mu1-CRR995112.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Mu1-CRR995112.2x36mers.noMT.bwa.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=LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Mu2-CRR995113.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Mu2-CRR995113.2x36mers.noMT.bwa.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=LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Mu3-CRR995114.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Mu3-CRR995114.2x36mers.noMT.bwa.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=LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Pl2-CRR995115.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Pl2-CRR995115.2x36mers.noMT.bwa.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=LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.bam OUTPUT=LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.bam METRICS_FILE=LS70_Pl3-CRR995116.2x36mers.noMT.bwa.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &