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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Batch SA730 requires both tumor and normal BAM files for VarScan cancer calling #1003

Closed funnell closed 9 years ago

funnell commented 9 years ago

I'm seeing the error: Batch SA730 requires both tumor and normal BAM files for VarScan cancer calling

I have all my libraries listed as tumor (they are cell lines).

chapmanb commented 9 years ago

Tyler; Sorry about the issue. VarScan isn't a great choice for tumor-only calling as it really doesn't have a mode where it is calling somatic samples without matched normals.

We can feed tumor-only samples into VarScan germline calling, so I pushed a fix to make that happen so it won't error out.

Practically, I'd call tumor-only with a different caller like VarDict or FreeBayes. Or use MuTect with a normal panel (the background option https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#variant-calling) if you have something suitable. Hope this helps.