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

Answered

Follow

Martin Grasshoff

• 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?

0

• 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

  Comment actions Permalink

Please sign in to leave a comment.