bcftools fixref command

Open
#737 4 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
20/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start by reproducing the reported bcftools +fixref command with broken.vcf, /path/to/reference.fasta, and All_20151104.vcf.gz, then inspect whether the input and reference contain records compatible with the command options. Done means identifying why fixref produces only the header and confirming a corrected behavior or a clearly documented limitation.

Written by the indexing model from the issue text.

Description

needs-feedback

Hello,
I have been trying to use the fixref command to swap reference and alternate alleles. I used the basic command:

bcftools +fixref broken.vcf -Ov -o fixref.vcf -- -d -f /path/to/reference.fasta -i All_20151104.vcf.gz

For some reason, when I use this command the output file is truncated to only the header. I used this same command previously on the same file.

Thank you for insight

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.