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.
Contest error: mismatched contigs
I've downloaded bams from dbGaP, that were aligned to grch37. GATK Contest tool is saying mismatched contigs when using hg19.
- Is there a different reference I should use, if yes, which one?
- If I replace the header of the downloaded bams with a header from an hg19 bam, is that acceptable?
It seems like the tool might only look at the header to make sure everything is ok?