We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
HaplotypeCaller in GATK4 vs GATK3
I know that HaplotypeCaller in GATK4 is still in development, but I want to make sure this issue is known We're seeing very different behaviour between the HC in GATK3 and GATK4 when using targeted resequencing data. By design, and in contrast to exome seq., we have many reads that start in the same place (and so set --maxReadsPerAlignmentStart 0), but also many positions that are covered only by reads from one strand and not the other. HC in GATK3 was assembling these and handling them fine in most cases (except when the SNP was very close to read end), but GATK4 seems to not assemble those portions in many cases, even when the SNP is ~20 nt away from the end of the read. Is this known? We can provide sample data for reproducing this problem if needed.