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!
Some questions on QD
Hello GATK team,
1) For multi-sample VCFs, how is the
QD value computed by GATK when more than one sample is
non hom-ref? For instance in my case I will have different
QD=QUAL/AD, for different values of
AD. If I compute my own
QDs and I want to apply these filters, will it be reliable to do such filtering using my own
2) Is there a chance of getting a value different from
QD=QUAL/AD if a specific argument is specified when executing the variant calling function (i.e