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.
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