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caravagnalab / CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package
GNU General Public License v3.0
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input somatic mutation file #22

Closed sabrina0701 closed 1 year ago

sabrina0701 commented 1 year ago

Dear CNAqc team,

A silly question, for the input somatic mutation file, should I use all the alleles or only the alleles as PASS after filter?

Best wishes

caravagn commented 1 year ago

Hi @sabrina0701 You mean that you have a VCF file from some caller with a PASS status?

sabrina0701 commented 1 year ago

Yes, so should I filter the somatic mutation with PASS only? Thanks!

caravagn commented 1 year ago

That is what most people often do, but this is a variant calling issue, not related to QC. In general you are safe to do that though.