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

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?

python
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written by dzisis1986 • dzisis1986

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
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written by Nicolas Rosewick Nicolas Rosewick

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 ?

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written by dzisis1986 • dzisis1986

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

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written by dzisis1986 • dzisis1986

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