How do I calculate QD for multiple samples, if all samples are homozygous?
AnsweredHi.
For multiple samples the QD values are calculated using the AD values of samples with a non hom-ref genotype.
https://gatk.broadinstitute.org/hc/en-us/articles/360041414572-QualByDepth
I have a small set of samples and all samples are either homozygous for the alternative allele or have no call for this variant.
How should I calculate the QD value in this case?
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Official comment
Hi Martin Grasshoff,
It's not possible to calculate QD for that case:
This annotation can only be calculated for sites for which at least one sample was genotyped as carrying a variant allele.
You'll have to look into using a different annotation for these sites.
Best,
Genevieve
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