Quantcast
Channel: Ask the FireCloud Team — GATK-Forum
Viewing all articles
Browse latest Browse all 1147

filtering a trio joint VCF based on GT DP

$
0
0

Hi

I have a joint VCF with a trio of samples in it, and would like to only retain those sites where all 3 samples have at least DP >=10
in their respective GT FORMAT field.

I have been trying to do this with VariantFiltration, but i can't figure out the correct command line to use.
Can you please recommend a command line that would achieve this?

Thanks
Severine


Viewing all articles
Browse latest Browse all 1147

Trending Articles