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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.
CalculateGenotypePosteriors and excess heterozygotes
In a partially inbreeding species we found an excess of called heterozygotes (a peak of observed/expected heterozygosity = 1.0). Is this because of CalculateGenotypePosteriors? Can we turn this off? Or better yet, can one set a prior for called heterozygosity / expected heterozygosity (an expected distribution of the inbreeding coefficient)?
The histogram of observed/expected heterozygosity is attached (with the low tail truncated).