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.
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?