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.
`MalformedReadFilter` seemingly overly aggressive?
I recently came across(blog post) a scenario in which a subset of my reads had triggered the
MalformedReadFilter during indel realignment. I'm curious to know about the definition of "malformed", as whilst invalid, I wouldn't have described incorrect mate names and alignment positions for unmapped reads as "malformed" and capable of causing job crashes...
Not a bug - I'm just curious to know of any implementation details or reasoning about the