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tasks/CNVkit.wdl
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| /root/miniconda2/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf | /root/miniconda2/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf | ||||
| /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf | /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf | ||||
| cp ${sample}.call.cns ${sample}.call.cns.bed | |||||
| #gain and loss | |||||
| cat ${sample}.call.cns | awk -v OFS='\t' '{ if ($6 > 2) print $0, "gain"; else if ($6 < 2) print $0, "loss"; else print $0 }' > ${sample}.call.cns.bed | |||||
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