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As I said in my last post about splitting my 11 samples from the recalibrated VCF file. I now have a different question which is how to set up a criteria to select variants from this 11-sample-combined VCF. My criteria would be DP >= 20 and # of ALT reads >= 10. I know the AD is the sum of both REF and ALT reads, but I was wondering if there's any way to select by the # of ALT and DP >=20?
Should I use the "-T SelectVariants" or "-T VariantFiltration"? I am using GATK 2.5 on a remote Mac OS X server by the way.