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.

Does GATK work with polypolids?

Hi, I would like to use GATK for SNP variant and indel variant calling in wild relatives of a crop plant. I have a good reference genome for the diploid crop where I could map my reads but my species where I would like to call the SNPs are di- tetra and hexaploid. I wanna trace there ancestry. Can I use GATK as a platform to call the genome wide SNPs?

Answers

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