Error: Merging ped and map files by PLINK
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9 months ago
X.Y.Zebby ▴ 20

Hello

I have two populations (ped and map files) that I want to merge in a file. I used PLINK software to reach my aim. But I faced an error in my work. I used "--allow-no-sex" or "--must-have-sex" in my code, but I cannot run again. My friend can run the below code without any error. We used the same PLINK version. I don't know that it is important or not his laptop is 32 bit.

Can you please guide me how to solve this error? Thanks

shell("plink --file s.QC --merge q.QC.ped q.QC.map --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --pig --recode --out qs.QC")

*Error: When ambiguous-sex samples with phenotype data are present, --make-bed/--make-just-fam/--recode/--write-covar usually cannot be combined with other commands. Split them across multiple PLINK runs, or use --allow-no-sex/--must-have-sex.

Warning message: In shell("plink --file s.QC --merge p.QC.ped p.QC.map --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --cow --recode --out ps.QC") : 'plink --file s.QC --merge p.QC.ped p.QC.map --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --cow --recode --out ps.QC' execution failed with error code 5*

SNP plink merge • 263 views
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