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.
Paired End Reads Overlap-Variant Call foreward/reverse reads with high error-rates
Moin from Kiel,
we have an urgent question we currently analyze variants from exon based on amplicons. The short exons are covered by the end of the foreward and reverse read. Unfortunately the error-rate at the end of the reads is quite high. So the region with the high error-rate of both reads covers the exon region. Is reliable call still possible (excluding softclipped reads, reads with low quality,...) due to the high coverange of amplicon-data >20k reads per position. Attached an example from igv (softclipped reads shown as well).