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tasks/CNVkit.wdl
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| # Prepare the target bed | # Prepare the target bed | ||||
| #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed | #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed | ||||
| /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -g access.bed | |||||
| /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method wgs -g access.bed | |||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn | /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn | ||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn | /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn |
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