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!