We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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.

Answers

Sign In or Register to comment.