1 changed files with 2 additions and 3 deletions
+ 2
- 3
tasks/CNVkit.wdl
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| String? fasta | String? fasta | ||||
| File ref_flat | File ref_flat | ||||
| File bed_file | File bed_file | ||||
| String method | |||||
| File hrd | File hrd | ||||
| File tumor_bam | File tumor_bam | ||||
| File tumor_bam_index | File tumor_bam_index | ||||
| if [ ${normal_bam} ]; then | if [ ${normal_bam} ]; then | ||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| --normal ${normal_bam} \ | --normal ${normal_bam} \ | ||||
| --method ${method} \ | |||||
| --method wgs \ | |||||
| --fasta ${ref_dir} \ | --fasta ${ref_dir} \ | ||||
| --annotate ${ref_flat} -p $nt \ | --annotate ${ref_flat} -p $nt \ | ||||
| --drop-low-coverage \ | --drop-low-coverage \ | ||||
| # 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} --method ${method} -g access.bed | |||||
| /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method wgs -g access.bed | |||||
| /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}.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 coverage ${tumor_bam} ${sample}.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn |
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