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input somatic mutation file #22

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sabrina0701 opened this issue Apr 3, 2023 · 3 comments
Closed

input somatic mutation file #22

sabrina0701 opened this issue Apr 3, 2023 · 3 comments
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@sabrina0701
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sabrina0701 commented Apr 3, 2023 •
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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
@sabrina0701 sabrina0701 changed the title inou input somatic mutation file Apr 3, 2023
@caravagn caravagn self-assigned this Apr 5, 2023
@caravagn caravagn added the help wanted Extra attention is needed label Apr 5, 2023
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caravagn commented Apr 5, 2023

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

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

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caravagn commented Apr 6, 2023

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.

@caravagn caravagn closed this as completed Apr 6, 2023
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