UnifiedGenotyping, HaplotypeCaller and PhasebyTrasmission

Giuliano

Hi to all

I began a variant analysis from 4 family related exome-seq samples in which a patology seems to be related to a polimorphism. I am just wondering which variant calling tools is better to use and if applying PhasebyTrasmission refinement is the correct way (in PhasebyTrasmission analysis does the read group that I assigned to bam file play a role in definition of the relation or I have to use just the ped file?).

Best
Giuliano

Geraldine_VdAuwera

Hi Giuliano,

To help you decide between the variant callers, please have a look at our Best Practices document:
http://www.broadinstitute.org/gatk/guide/article?id=1186

There is a section that explains what are the strengths and weaknesses of both tools.

Regarding genotype refinement, please look at the presentations from our recent user workshop:
http://www.broadinstitute.org/gatk/guide/events?id=2038

Only the PED file is used to determine the relationship between samples/ family members.