DReichLab / DReichLab/AdmixTools
bad chrom
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- Dominant language
- C
- Stars
- 235
- Forks
- 76
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Description
Hi there,
I would like to use convertf to convert from vcf to eigenstrat to test hybridization using ADMIXTOOLS. The problem is, that my chromosome IDs don't refer to actual chromosomes but to scaffolds.
When I run converf I get an error saying:
warning (mapfile): bad chrom: 100
I realized that when I set all chromosomes to 1, sort the variants and remove those that are duplicate, convertf works. But I dont want to loose the actual snp order. Also I'd prefer not to remove duplicate variants...
Is there any way to circumvent this and to be able to generate an eigenstrat file without having to change the chrom IDs?
Thanks in advance!
Contributor guide
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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.
Research direction
Start by reproducing the conversion with convertf using scaffold chromosome IDs, including the reported bad chrom: 100 warning. Check how convertf handles chromosome IDs, ordering, and duplicate variants during VCF-to-eigenstrat conversion; done means the conversion succeeds without renaming chromosomes, sorting away order, or removing duplicates.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100