We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
ExcessHet filtering in cohorts with family members
This post mentions that the first step in Best Practice VQSR filtering involves hard filtering on ExcessHet. The post also states that "ExcessHet filtering applies only to callsets with a large number of samples, e.g. hundreds of unrelated samples."
I have a cohort of 170 samples from 70 families. Each family consists of either a trio, duo or singleton, depending on who I could recruit. Some of these families are consanguineous. Each family has a different undiagnosed rare disease and I am trying to find the causal variant in each family. The whole 170 samples were aligned and variant called following GATK Best Practices. No pedigree file was used during variant calling. In a sample VCF from this cohort, there are 4.9 Million variants, 124'00 of which are flagged as 'ExcessHet'. My question is: can I treat the variants flagged as 'ExcessHet' as likely false positives or does the fact that my cohort consists of multiple unrelated families make the 'ExcessHet' filter unreliable?
I don't really understand why ExcessHet filtering is needed in the VQSR workflow, so if you could explain what ExcessHet does in this context, this would be great!