Question about criteria selecting variants
Posted in Ask the GATK team | Last updated on


Comments (15)

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.


Return to top Comment on this article in the forum