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.

basic bam-readcount function in GATK?

I'm hoping to find a GATK solution to replace the use of bam-readcount in a pipeline.

For a given BAM, and a given position, I need to get the number of reads for each base (reference and alteration), as well as the overall read depth at that position.

If this functionality is present, pointers to the appropriate classes/methods would be greatly appreciated.

I apologize if this is an obvious question. This is my first rodeo.


Sign In or Register to comment.