Heads up:
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!

Mapping a locus to a chromosome in a genome


I am currently working on a maize mutant and wild type data. I have the DNA-Seq data for these samples and I am currently using the GATK pipeline to analyze the data. I am trying to map the mutation to a specific chromosome so that I can identify a specific region on the chromosome. I have finished the analysis using the Haplotype caller for both the mutant and the wild type samples. I wanted to know whether there is any specific command or tool in GATK which I could possibly use to map the locus of mutation on a chromosome in one or two steps. Thank you


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