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tasks/CNVkit.wdl
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| @@ -29,7 +29,7 @@ task cnvkit{ | |||
| /root/miniconda2/bin/cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats | |||
| # Derive each segment's absolute integer copy number, ploidy must be int value | |||
| PURITY=3.3 | |||
| PURITY=0.3 | |||
| /root/miniconda2/bin/cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns | |||
| /root/miniconda2/bin/cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns | |||
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