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.
All SNPs are heterozygous
All of my whole-genome sequenced individuals are a cross of different outbred lines with one reference line - effectively identical to the reference genome used for read mapping and variant calling. Thus, effectively all SNPs are heterozygous relative to the reference genome.
Should I alter the settings on the Unified Genotyper to maximise detection of these kind of variants ?