To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Joint calling in trios using UnifiedGenotyper

Hi,

I have exome data for a few sets of parent-offspring trios, in which offspring have phenotypically related but probably genetically different diseases. Their parents are unaffected so I am particularly interested in identifying de novo mutations. My plan was to analyse each individual separately up to the variant calling phase and then to input three (mother, father, child) analysis-ready BAMs into the UnifiedGenotyper along with a ped file. My questions are:

1) Can you tell me whether the UnifiedGenotyper uses pedigree information in the ped file to call genotypes more accurately? In other words, is this better than calling variants jointly without supplying the ped file? If not, does GATK recommend any external tools for doing this step?

2) It is better to call variants jointly using all the trios (even though they are not related and probably don't share the same disease-causing mutations)?

Best wishes,

Kath

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Kath,

    1. No, the UG does not make use of pedigree information. Several GATK tools use PED info downstream of calling, for example for phasing, evaluating mendelian violations and so on.

    2. You should definitely call members of each trio together. As for calling all trios together, it is unlikely to yield any added benefit if the genetics of the diseases are unrelated, but it can't hurt to do it if you have the computing power.

  • KathKath Member

    Thanks for your help,
    Kath

Sign In or Register to comment.