Outputting DP4 flag in GATK

Question

[Jautis]

Hello, is there any way to output DP4 (as well as DP) while using GATK's Haplotype Caller to call variants?

Thanks!

Answer 1

[Santosh Anand]

Annotate the variants for StrandAlleleCountsBySample using VariantAnnotator tool.

[Jautis]

So that appears similar to DP4, but I need it in DP4 rather than the set of 8 values StrandAllelesCountsBySample would give. I'm piping the vcf into another program and I'm not familiar enough with how that one runs to modify it to use SAC instead.

[Santosh Anand]

I am not sure if you can do that directly. However, you have all the required info, and you can generate an intermediate vcf file (or pipe it directly) using shell-commands.