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How to treat heterozygous GATK calls on haploid chromosomes (sex chrom in males)

How do people normally treat heterozygous HaplotypeCaller variants on haploid chromosomes, like sex chromosomes in males?

Do you usually omit such calls? Or is there a method to resolve the genotypes. I assume GATK is sophisticated enough that most of the true positive calls on these chromosomes would be outputted as homozygous genotypes.

haploid gatk haplotype caller snps
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updated by monicapenon • monicapenon • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

Don't forget the pseudoautosomal regions.

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written by WouterDeCoster WouterDeCoster

Those should be treated as diploid, so heterozygous calls are fine.

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written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

From my experience, without any adjustments for sex chromosome signals, they are mostly called as homozygous, as one would expect. If I see heterozygous calls, I assume error due to mis-alignments. Many downstream programs 'don't want to know' about the sex chromosomes, so, I feel that genetic data from these has been mostly overlooked in association studies.,

You may get a better response for this question on the GATK forum.

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written by Kevin Blighe Kevin Blighe

1 answer

How did you solve the issue of treating heterozygous variants in the X chromosome inside NON-pseudoautosomal regions for males?

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written by monicapenon • monicapenon

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