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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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Applying internal filters to outputs before running SomaticSeq #123

Closed ronkesm closed 5 months ago

ronkesm commented 1 year ago

Hi,

I was wondering how useful it is to apply the internal filters of SomaticSniper, Varscan2, mutect2 etc. before inputting them into SomaticSeq? I compared outputs from CaVEMan (alone) and SomaticSeq with filtered Varscan2 + SomaticSniper and Muse and found that variants under 0.1 VAF were completely absent from the latter (even though it is relatively high coverage data ~60-70X).

Thanks

litaifang commented 11 months ago

Depends..... I usually don't filter for each caller before hand. I can always filter them afterwards. Once aggregated from all the callers and features extracted from the bam files, there are additional criteria you can decide on.