The current GATK version is 3.2-2

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

# Does setting the -out_mode flag in UnifiedGenotyper differently has different effect when doing VQSR

Posts: 0Member
edited October 2012

Hello,

Does VQSR behave differently when the -out_mode flag in UnifiedGenotyper is set to EMIT_VARIANTS_ONLY as compared to EMIT_ALL_CONFIDENT_SITES. I think by using EMIT_ALL_CONFIDENT_SITES we might give VQSR more information to train the model, but I may be wrong. Can someone please help me with this ? Thanks.

cheers, Rahul

Post edited by Geraldine_VdAuwera on
Tagged: