Annotate ALT field with N as a value

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with vcfannotate.c and the vcf_setter_al code mentioned in the report, then reproduce annotation of a VCF record whose ALT field is N against a dbSNP BCF. Compare that behavior with records using A, G, C, or T, and document or correct the code path that explains the difference.

Written by the indexing model from the issue text.

Description

needs-feedback

I am working on annotating a vcf file using a bcf dbSNP.
But it seems that records with N as an ALT field don't get annotated. But surprisingly to me, records with false A,G,C, or T characters get annotated and corrected. I assume there is a place where this logic is implemented, but I can't find it.
Can you point me to why this happens? Also I inspected the vcf_setter_al code here https://github.com/samtools/bcftools/blob/develop/vcfannotate.c
with no luck.

Thanks in advance

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

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