If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.
GATK resource bundles scattered_calling_intervals exclude small contigs
I was just going over some Haplotypecaller and VQSR results generated using your best practices Cromwell workflows, and found that the scattered_calling_intervals files you provide (and which those workflows use to operate over) do not cover the whole genome. For hg38, chrM and all of the alt/unplaced contigs are excluded. For b37, chrY is also excluded.
This seems like a fairly major bug that would cause people running your best practices to lose a good number of potentially important variants.