Hi, I would like to extract variants for on sample only if its genotype quality (GQ) is above cutoff.
I have tried this:
$pathToGATK \ -T SelectVariants \ -R ref \ --variant inVCF \ -sn mylib \ -select "vc.getGenotype('mylib').GQ > 10.0" \ --selectTypeToInclude SNP \ --out outVCF
Unfortunately, this command outputs absolutely no variant (the VCF header is ok). No error message occured. Is some one could help me?