If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
SNP filtering for haploid genomes
Does the GATK team have any recommendations for filtering SNP data for haploid genomes? Our team works with microbial eukaryotes, both haploid and diploid and we have used the GATK v3 best practices for filtering for the latter. [VQSR was not possible, since we do not have access to a truth/high confidence SNP set.]