Feature for encoding and decoding sex of samples/genomes in VCF header
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start with the linked SourceForge discussion and the proposed bcftools reheader --add-sex and bcftools query --list-samples-with-sex interfaces. Clarify how sex should be represented in the VCF ##SAMPLE header and whether bcftools convert must preserve it for sex-aware formats. Done means the representation, input/output format, and conversion scope are agreed before implementation.
Written by the indexing model from the issue text.
Description
I would like to encode the sex of the samples contained in a VCF in the VCF header.
Based on the discussion at http://sourceforge.net/p/vcftools/mailman/message/28587354/, it appears that the best way of doing this in the absence of a ##GENOME field would be to encode sex using the ##SAMPLE field.
So, what I'm envisioning are additions to bcftools that work in the following way:
bcftools reheader --add-sex sex_file file.vcf.gz
bcftools query --list-samples-with-sex > sex_file.2
, where sex_file and sex_file.2 would not differ, and where sex_file would look like this:
sample sex
samp1 female
samp2 male
samp3 male
...
Ideally, sex awareness would also be added to the bcftools convert tools that convert to and from sex-aware file formats (for example Impute2 format).
What do people think?
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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