Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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?

Answered
0

1 comment

  • Official comment
    Avatar
    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.

    Best,

    Genevieve

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk