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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