Question Regarding SNP Count After Merging Genotype Files
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- Dominant language
- C
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- 207
- Forks
- 61
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Description
I hope this message finds you well.
I recently merged two identical genotype files and noticed that the resulting merged files had fewer SNPs than expected. Initially, each file had 1,233,013 SNPs, but after the merge, both the SNP and .geno files had only 1,196,712 SNPs.
I ran a quick check using wc -l *.geno to count the lines, and the result was consistent across both files post-merge. Could you please help me understand why this reduction in the number of SNPs occurred?
I would appreciate any insights you might have regarding this.
Looking forward to your response.
Best regards,
Jiashuo
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Research direction
The issue names no source file, test, command, or merge entry point beyond wc -l *.geno and the reported SNP counts. Reproduce the merge with the two identical genotype files, then trace the merge tool's handling of SNP records; done means explaining the reduction or documenting a confirmed defect and its expected result.
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