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.
Unified Genotyper: Maximum sensitivity
I'm seeing Mendelian errors in small but significant proportion of my unified genotyper calls. For many instances the SNP is called incorrectly as a homozygote even though there are some reads of the second allele. How can I set unified genotyper to be more sensitive ?