How to understand if a GWAS sample comes from Chromosome X or Y

Question

[dzisis1986]

I have a GWAS sample like this https://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs001672/analyses/phs001672.pha005197.txt.

I want to create a Python script that will be able to declare if the chr23 is referred to X or Y independent to the description which says that its X. I was thinking of checking the column with variant Position and if this is bigger than the boundary of chromosome Y (58000000) then that means that it is chromosome X.

Can we do something like that in Python ?

Do you have an alternative?

[Nicolas Rosewick]

FYI most of the time chromosomes are coded like this. Do you have a dataset with chr23 = chr Y ?

X    X chromosome                    -> 23
Y    Y chromosome                    -> 24
XY   Pseudo-autosomal region of X    -> 25
MT   Mitochondrial                   -> 26

[dzisis1986]

No, I just have the one with chrX = chr23. I was trying to find a GWAS with chrY but cant find one ! But i was reading a post saying that there are cases where chrY is declared as 23. maybe i didnt understand well . So from you opinion and some other annotation tools i can see that the above answer is accepted also in GWAS. Just to confirm, deffinitely there is no chance to see chr23 = chr Y ?

[bk11]

Standard tools like PLINK use the above codes mentioned by Nicolas Rosewick. It is right that chr23 is not chrY. You can download data from 1000 genome population which includes all chromosomes. See the link below- http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

[dzisis1986]

yes you are right! I agree. I found also s GWAS dataset to confirm it! Thank you very much