Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Joint calling in trios using UnifiedGenotyper

KathKath Posts: 36Member

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

Sign In or Register to comment.