Question: How to treat heterozygous GATK calls on haploid chromosomes (sex chrom in males)
0
gravatar for QVINTVS_FABIVS_MAXIMVS
21 months ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.3k wrote:

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.

ADD COMMENTlink modified 5 days ago by monicapenon0 • written 21 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
1

Don't forget the pseudoautosomal regions.

ADD REPLYlink written 21 months ago by WouterDeCoster42k

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

ADD REPLYlink written 21 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
0
gravatar for monicapenon
5 days ago by
monicapenon0 wrote:

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

ADD COMMENTlink written 5 days ago by monicapenon0
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