How do I calculate QD for multiple samples, if all samples are homozygous?

Answered

May 19, 2021 16:02

Hi.

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?

1 comment

Official comment
Genevieve Brandt (she/her)

June 02, 2021 18:39

Edited
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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