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.
Analysis in the recent Cell paper by Hodis et al
in the recent Cell paper by Hodis et al (Broad Institute) using GATK for somatic mutation calling, authors report filtering indels that were "supported by reads with a high average number of additional mismatches and calls made in genomic loci covered by reads with a high average mismatch rate and low base quality". It is pointed out in the paper that this is a part of GATK. I haven't been able to locate the corresponding algorithm. Could you please point me to the walker/function?