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.
Mutect2 md5 error
Using the standard mutect2 commands from the docs I get the error seen below. My reference file dictionaries were all made automatically from mutect version 1.4. Is there a workaround for this md5 problem. I tried an awk command to take out the m5 column from the fast.dict file, but that didnt work. Is there a flag that I'm not seeing to avoid this MD5 column check because for my purposes if the length is the same its likely that they are the same contig? Any help would be greatly appreciated.