The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

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

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

Triggering genotype calls at HapMap sites

genegene Member Posts: 17
edited September 2012 in Ask the GATK team

Hi,

I would like to trigger calls at HapMap sites even if they are HOM_REF in my sample. I used to accomplish this in an older GATK version with the following parameter passed to the UnifiedGenotyper: -B:trigger,VCF hapmap.vcf
Right now I am using version 1.6 of the GATK.
How could I accomplish exactly the same with this new version?

What I am trying to do (when doing VariantEval on the detected SNPs) is to obtain GenotypeConcordance for all:
HETs, HOM_REFs, and HOM_VAR.
Currently I only get the concordance values for HETs and HOM_VAR on the VariantEval output.
Asked in a different way, how could I get the 'n_true_HOM_REF_called_*' fields populated in the VariantEval?

Thanks for your help,
Gene

Post edited by Geraldine_VdAuwera on

Answers

Sign In or Register to comment.