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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Alternative basecallers with GATK?
We are working on various non-model organisms without snp databases available. Of course this makes BQSR a problem, and we're not entirely convinced by the "bootstrapping" method.
However the question came up if alternative base callers can't solve this problem at least partly? There are of course many, such as Ibis, AYB and BayesCall, that can be used as an alternative to Bustard. Some of these programs supposedly have a better quality score distribution . Have these ever been tested with GATK?
1 Ledergerber, Christian, and Christophe Dessimoz. 2011. “Base-Calling for next-Generation Sequencing Platforms.” Briefings in Bioinformatics 12 (5): 489–97. doi:10.1093/bib/bbq077.