Question Regarding SNP Count After Merging Genotype Files

[zhangjsyeah]

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

[bumblenick]

Jiashuo Please send me your logfile (stdout) \

…

On Sun, Sep 28, 2025 at 10:43 PM jiashuo zhang ***@***.***> wrote: *zhangjsyeah* created an issue (DReichLab/EIG#114) <#114> 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 — Reply to this email directly, view it on GitHub <#114>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77B3NWAWNNVWCFKNVPPL3VCMFHAVCNFSM6AAAAACHXYH3RGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGQ3DEOJZGYYTGOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>