Best practices for converting plink bed bim fam to geno snp ind
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 20/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
The issue names PLINK and convertf but no repository files or tests. Review the existing convertf workflow and project documentation to determine the supported conversion and merge path, including whether allele order affects the resulting SNP data. Done means a documented, validated best-practice workflow.
Written by the indexing model from the issue text.
Description
Is there currently a best practice for adding plink bed bim fam samples to geno snp ind datasets.
I've always 1st converted geno snp ind to plink using convertf , merged all plink data in plink, then converted bed bim fam to ped map pedind and back to geno snp ind using convertf.
Sometimes I feel this is not the best way to do it though.
Also, FYI plink doesn't preserve allele order and I wasn't sure if allele order in snp files is important to AF calculations, so I have as a matter of practice always re-aligned allele order in snp files (messed up by conversions from plink) to match dbSNP and ensure that col 5 is REF and col 6 is ALT in snp file
- Dominant language
- C
- Stars
- 236
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
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