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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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Put FILTER in FILTER field, not INFO #130

Closed bangbangphil closed 3 years ago

bangbangphil commented 3 years ago

Hi,

Is there a way to write to FILTER field column? I know I can get FILTER fields from the input VCF writtten in INFO as a list value, put what I would need is to write a particular FILTER tag from the input VCF into the FILTER column of the output VCF. Is that possible?

thank you for your help,

Philippe

brentp commented 3 years ago

Hi, that's not possible. You'd have to use a downstream script to take the (newly added) filter from the INFO and put it in the FILTER field.

bangbangphil commented 3 years ago

Ah ok, guess I'll do just that. Thanks for the quick reply!

De : Brent Pedersen notifications@github.com Envoyé : 3 novembre 2020 09:00 À : brentp/vcfanno vcfanno@noreply.github.com Cc : Philippe bangbangphil@hotmail.ca; Author author@noreply.github.com Objet : Re: [brentp/vcfanno] Put FILTER in FILTER field, not INFO (#130)

Hi, that's not possible. You'd have to use a downstream script to take the (newly added) filter from the INFO and put it in the FILTER field.

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brentp commented 3 years ago

no problem. I do see the utility of what you are requesting, but I don't want vcfanno to collapse under its own complexity.