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.
Can I persuade GATK to resolve 2 indels as 3 SNPs?
I have the following two haplotypes in my data:
GATK is (not incorrectly) resolving this as an insertion of T after position 1 and deletion of T at position 6. However, I would really like this to be resolved as 3 SNPs at positions 3 (G/T), 4 (A/G) and 6 (T/A). Is there some parameter I can change to get GATK to resolve things in this way?