Option to move filter to format in merge

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
42/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with the merge command and its existing -F/--filter-logic option, then trace how merged VCF records represent sample filters. Check how FORMAT fields are constructed and determine the expected per-sample filter output; done means the option preserves which samples had filters and the behavior is covered by relevant merge tests.

Written by the indexing model from the issue text.

Description

enhancement

The filter logic in merge is really nice

-F, --filter-logic x|+            Remove filters if some input is PASS ("x"), or apply all filters ("+") [+]

but I want to suggest another option which would move the filters to a new FORMAT field. My use case for example is I have merged the VCF for four samples and would like to be able to check which samples had a filter at a position. At the moment, using "+" I just know that at least one sample had a filter, but not which sample.

If there is an alternate way of doing this I would love to know.

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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