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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