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!
Well-calibrated likelihood that a variant is truly heterozygous rather than homozygous?
I have whole genome sequencing data, and I am trying to assemble a list of sites which are heterozygous with high confidence.
VariantRecalibrator seems to estimate two distributions: a (0/0) distribution and a (0/1 ∪ 1/1) distribution. So, I can quantify my confidence that a site is not 0/0.
However, I don't see any way to quantify confidence that a site is 0/1 as opposed to 1/1. I have not found any information about this in the documentation page for the tool, the FAQ page on setting its options, the tutorial, the forums, or the DePristo et al 2011 paper.
So, I have two questions:
Is it possible to calculate a well-calibrated likelihood ratio between the 0/1 and 1/1 possibilities, using VariantRecalibrator or another tool?
How do people generally go about performing tasks like mine, where they are trying to make a list of specifically heterozygous sites, excluding homozygous sites?