Issue when converting from plink to eigenstrat using convertf
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- Dominant language
- C
- Stars
- 207
- Forks
- 61
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Description
Hello,
I have a vcf file and a plink file with 5,758,371 positions. The vcf was converted to plink using the plink software, and then, I used convertf to convert the plink (bed) into an eigenstrat file. After converting to eigenstrat, my eigenstrat file has 5,757,704 positions. Apparently, the convertf run had no issues since the .err file came out empty. Why would I be losing 667 positions? Thanks in advance
Best,
Jose Antonio
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Research direction
No source files or tests are named. Start by reproducing the PLINK-to-EIGENSTRAT conversion with the reported counts and inspect convertf's output and error handling; determine which 667 positions are omitted and document the cause or required input constraints.
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Assessment
- Tech stack
- c
- Domain
- data, tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100