Problems with sex determination with genotyping data Illumina

Question

[vicbp1]

Dear all,

I have problems with the sex determination of the samples from genotyping data 2.5M Illumina.

I made a filtering for Y chromosome SNPs (> 2000 snps) and using PLINK:

plink --file file_Crom_Y --make-bed --mind 0.1 --geno 0.1 --out output --noweb

All the snp were excluded. When I check the frequency with this dataset the "number of chromosomes" was zero >

CHR              SNP   A1   A2          MAF  NCHROBS
  24       rs11575897    0    C           NA        0
  24        rs2534636    0    C           NA        0
  24       200610-249    A    G           NA        0
  24       rs35840667    C    A           NA        0
  24        rs2253109    A    G           NA        0
  24       200610-252    T    C           NA        0
  24       rs35067692    0    T           NA        0
  24       200610-360    0    T           NA        0
  24        rs9786608    0    0           NA        0
  24        rs2058276    A    G           NA        0
  24       rs13303871    0    G           NA        0
  24       rs28813670    T    G           NA        0
  24       rs11799203    A    G           NA        0

but like above, the file has Alleles but non chromosomes, so I thought that the samples were women.

And finally when I did a sex check in Plink using the X chromosome, the result was 6 men and 9 women.

Can anybody help me to understand this problem?

Is it a genotyping error?

Answer 1

[Leonida Monaco]

Plink uses for X Chr 23 for Y 24 and for XY 25 . I think this was your problem, but I am not so sure