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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Further information about MuTect2 filters (clustered_events, homologous_mapping_event etc.)
Dear GATK developers,
We are using MuTect2 for variant calling and we have noticed that several variants fail to pass filters such as clustered_events, homologous_mapping_event, str_contraction and t_lod_fstar. We have reasons to believe that at least several of these variants could be incorrectly filtered out by MuTect2. For example, several variants that are positioned very closely to each other have been filtered out as clustered_events, although they have been previously verified and confirmed using Sanger sequencing.
I am aware that these filters are briefly described in the VCF file header (e.g. ##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">). However, I would like to ask whether there are any better definitions and further information about these filters and whether there are ways of manipulating or disabling them.
Thank you for your help.