1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/CNVkit.wdl
View File
| @@ -38,8 +38,8 @@ task cnvkit{ | |||
| /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.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn | |||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.target.bed -o ${sample}.T.targetcoverage.cnn | |||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn | |||
| /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t my_baits.target.bed -a my_baits.antitarget.bed | |||
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