Hi, I wanted to double check my methods for some targeted capture data. I ran 96 samples through UG to produce a multisample VCF. I separated snps and indels into separate files using SelectVariants, and applied filters:
For snps "QD < 2.0", "MQ < 40.0", "FS > 60.0", "HaplotypeScore > 13.0", "MQRankSum < -12.5", "ReadPosRankSum < -8.0"
For indels "QD < 2.0", "ReadPosRankSum < -20.0", "InbreedingCoeff < -0.8", "FS > 200.0"
I then went back through with SelectVariants, pulling out each sample one at a time into their own filtered VCF.
My results are... lets say, wrong. I am wondering if it would be better practice to select each sample first and then apply the filters, or if it does not matter and my errors lie elsewhere. Thank you.
