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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
BSD 3-Clause "New" or "Revised" License
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Output normal sample in the VCF #14

Closed bcantarel closed 1 day ago

bcantarel commented 1 month ago

It would be great if deep somatic could output the normal sample in the VCF similar to Mutect and other somatic callers, this to ensure end-users that their somatic variants have little (1 or 2) or no reads in the normal sample.

kishwarshafin commented 1 month ago

hi @bcantarel ,

Currently, the VCF is tagged with "GERMLINE" and "SOMATIC" for each variant. However, please do not use the output of DeepSomatic for downstream germline variation analysis. We exclude a lot of variant that appear to be germline in pre-processing without reporting them in the VCF. The best idea is to run DeepVariant separately on the normal sample and use it for analysis.

Also, apologies for the delayed response.

pichuan commented 1 day ago

Hi @bcantarel , I'll close this issue now. Feel free to reopen or open a new issue if you have any follow up questions.