If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

VariantFiltration not filtering 'NA' QD values when filtering QD

I am running VariantFiltration with "--filter-expression "QD < 2.0"

I then run SelectVariants with "--exclude-filtered".

In the output file, all SNPs with a numeric QD value of < 2.0 are indeed filtered out by VariantFiltration and removed by SelectVariants. But a large number remain with the QD value, "NA". I'm seeing these when I run VariantToTable and sorting the QD column from small to large.

Is this supposed to happen? I am hard-filtering SNPs as I'm using non-human genomes, with a view to using decent calls in BQSR and later VQSR. If QD = NA and does not have a value, surely this does not bode well?

Many thanks in advance.


Sign In or Register to comment.