Add copy number to somatic exome workflow

genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

MIT License

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Closed jasonwalker80 closed 5 years ago

jasonwalker80 commented 6 years ago

WES copy number calling
- probably with varscan
- https://github.com/genome/cncwl
- This re-runs varscan on the bam. Investigate whether the varscan output files being created in detect variants can be re-used for this purpose. (probably)
WGS copy number calling
- uses copyCat

jasonwalker80 commented 5 years ago

CNVkit is available for either WES or WGS.