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# Triggering genotype calls at HapMap sites

Posts: 17Member
edited September 2012

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?

Gene

Post edited by Geraldine_VdAuwera on
Tagged:

Hi Gene, please have a look at the documentation for the UnifiedGenotyper, specifically the --output_mode argument.

Geraldine Van der Auwera, PhD

• Posts: 17Member

Hi Geraldine,

• If I set --output_mode to EMIT_ALL_SITES I get the calls at HapMap HOM_REF sites but also every single base in the intervals indicated by -L file.bed gets called. This is undesirable.
The previous -B:trigger,VCF hapmap.vcf argument would trigger aditional calls ONLY at those site that were HOM_REF in the HapMap reference. Is there a way to obtain this same effect with a different combination of parameters (without having to call SNPs at every single base)?

Thx,
Gene