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Does the UG call variants in pseudoautosomal regions correctly?

evakoeevakoe Member Posts: 33

Dear GATK team,

when I use the UnifiedGenotyper to call variants in chrX and/or chrY with ploidy=2, does the program call the variants and genotypes in the pseudoautosomal regions PAR1 and PAR2 correctly? More specifically, does the UG acknowledge that these regions are homologous on the X and Y chromosome, even though they differ in chromosomal position? If the UG does not take care of this by default, is there a way I can handle this? I read point 6 of this page, but I could not find the answer there:

Thanks alot

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,163 admin

    Geraldine Van der Auwera, PhD

  • evakoeevakoe Member Posts: 33

    Yes, if I understand correctly, the PAR regions of the Y are mapped to the corresponding positions in the X chromosome. So I want to call SNPs in the PAR regions in a male sample, I have to call in the regions chrX:60001-2699520 and chrX:154931044-155260560. Is that right? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,163 admin

    Yes, that's correct, but I believe you'll also have to call over the analogous regions in the Y chromosome, and you'll have to somehow manually merge variants corresponding to the same locations to get true het states if that's what you're after. We don't treat those locations in any special way - they're just different contigs to us and all merging/analysis of the PAR1 and PAR2 regions will have to be done by users or downstream tools.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,163 admin

    Thanks for the clarification, @Kurt, that sounds right.

    Geraldine Van der Auwera, PhD

  • evakoeevakoe Member Posts: 33

    Great thanks alot Kurt and Geraldine. This helped me much.

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