1 changed files with 6 additions and 5 deletions
+ 6
- 5
tasks/CNVkit.wdl
View File
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size | ||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} | |||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} --diagram --scatter | |||||
| /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf | |||||
| #/root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf | |||||
| /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf | |||||
| #/root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.cns -o ${sample}.diagram.pdf | |||||
| /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf | |||||
| /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.cns -o ${sample}.heatmap.pdf | |||||
| /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt | /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt | ||||
| /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt | |||||
| /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt | |||||
| cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt | cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt | ||||
| cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt | cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt |
Loading…