.snp file format
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Description
I wanna to understand if the v54.1_1240K_public.snp file column in Eigenstrat format represents "SNP ID","Chromosome","Position in centimorgans","Base-pair coordinate","ALT allele","REF allele"? or the last two column mean "REF allele" and "ALT allele"?
head(file):
rs3094315 1 0.020130 752566 G A
rs12124819 1 0.020242 776546 A G
rs28765502 1 0.022137 832918 T C
rs7419119 1 0.022518 842013 T G
rs950122 1 0.022720 846864 G C
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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 linked v54.1_1240K_public.snp file and its six-column examples, then compare them with the Eigenstrat format used by this repository. Done when the column order, including the REF/ALT interpretation, is explicitly confirmed in the issue or project documentation.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100