annotate ID for multi-allelic sites

Open
#2,264 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Reproduce the report with bcftools annotate -c +ID -a using the shown source and target records on bcftools 1.19. Compare annotation behavior for the G and T target lines; done means determining whether rs1258851236 should be copied to both records and documenting or correcting the observed result.

Written by the indexing model from the issue text.

Description

I found that ID column from multi-allelic site from a source file only transferred to the first allele in the target file.

My source annotation file:

chr21	5030278	rs1258851236	C	G,T	.	.	RS=1258851236

And my target file:

chr21	5030278	.	C	G	.	.	.
chr21	5030278	.	C	T	.	.	.

The command I used is as follows:
bcftools annotate -c +ID -a [source file] [target file]

And I got:

chr21	5030278	rs1258851236	C	G	.	.	.
chr21	5030278	.	C	T	.	.	.

Shouldn't the ID (rs1258851236) be annotated to both lines in the target file?

The version I used: bcftools_annotateVersion=1.19+htslib-1.19

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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from samtools/bcftools

All issues in samtools/bcftools

Similar issues

More C issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.