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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
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Output files when running Consensus mode #94

Closed wx-jiang closed 4 years ago

wx-jiang commented 4 years ago

Hi,

When I ran SomaticSeq in consensus mode on Mutect2 and VarScan vcf files, I got two Consensus files and two Ensemble files. Am I correct that the consensus files are common variants shared by Mutect2 and VarScan? If so, I have 500000 variants in consensus files while VarScan only called 80000 variants. If not so, would you mind explaining the output files more and how to fix my problem?

Thanks in advance!

litaifang commented 4 years ago

Consensus files contain everything. If you want to filter for calls that's been called by both VarScan2 and MuTect2, then there should be a field in the INFO column, e.g., MV=1,1 (M=MuTect, V=VarScan).

wx-jiang commented 4 years ago

Thanks!