Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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


1 comment

  • Official comment
    Genevieve Brandt (she/her)

    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.



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