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

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 • 1.9k views
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Don't forget the pseudoautosomal regions.

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

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2.1 years ago
monicapenon ▴ 10

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

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