(getpedgenos) bad geno <DEL>
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- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
- No merged PRs in 30d
Description
Hi, smartpca team. Thanks for developing such great software!
I imputed my .vcf file and converted them to .ped file for smartpca analysis. But there is an error:
I checked my .ped file and it did have <DEL> in it.
I don't know why the <DEL> appears and want to know what should I do to get my analysis going.
Thanks for any help!
JW
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 with the getpedgenos workflow and the reported .ped input, then determine where is introduced during VCF-to-PED conversion. Done means identifying the source of the invalid genotype and documenting or implementing a reproducible fix so smartpca analysis can proceed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100