Hello All,

I am not sure if I should go next or do I need to care about the decreased 'Total genotyping rate' reported by plink. Simply speaking, I used GenomeStudio2.0 to clean poor quality SNPs, then I recalculated the call rate of all the genotyped samples, the lowest genotype rate was > 98%, however,

when I used the following command to convert the lgen file to ped and map file, the plink delivered two messages 1. Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands treat these as missing. 2. "Total genotyping rate is 0.86", which was far less than the value calculated by GenomeStudio2.0...

I am wondering if issue 1 caused low genotyping rate reported here? I have checked the female Y genotypes, which were all with very low intensity, i.e. they were treated as missing genotypes by genomestudio, but plink reported issue1, so shall I just remove all those female Y snps?

> plink --lfile mydata --recode

I am not sure what caused the big difference regarding the "genotyping rate", anyone does have a clue?

Here is the first five lines of the lgen file

FID  sample.ID    SNP.Name      Allele1   Allele2
A      A1         1:103380393     G           G
A      A1         1:109439680     A           A
A      A1         1:118227370     T           T
A      A1         1:1183442       A           A
A      A1         1:118933200     G           G

and the fam file

A A-1 0 0 1 1
A A-2 0 0 2 2

and the map file

1       1:103380393     0       103380393
1       1:109439680     0       109439680
1       1:118227370     0       118227370
1       1:1183442       0       1183442
1       1:118933200     0       118933200

Many thanks in advance!