Transforming diploid GT on male X and Y chromosome to haploid

Question

[Michaela]

Hello,

maybe it is a well known fact, but I cannot find much information anywhere.

I am working on a bunch of gVCF files and struggle with the genotype representation in male X and Y chromosomes, which, to my understanding, is mostly represented as diploid, since the variant callers cannot really tell (except from few exceptions).

My question is, what is the best practice to convert the GT on those chromosomes to its haploid form? I have the information about sex per sample. I work in Hail so they provide a function to impute ploidy on the given chromosome as well.

However, is there already a tool/method which transforms the GT or am I meant to write the logic myself? Transforming the homozygous GT is straight forward, but transforming GT like 1/0 requires a bit more of a thought and I do not want to reinvent the wheel. Have I overlooked something?

Thanks for any advice!

Answer 1

[Michaela]

Hello,

if anyone needed an answer, I found a solution in the Gnomad python package. They provide a function adjust_sex_ploidy() which only takes a hail Matrixtable and a column field with the sex. The logic behind it can be found in their repo to get a better understanding!