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.
short read preprocessing in MuTect
Hi, I am using MuTect on paired tumor/normal exome data. MuTect pre_process low quality reads before somatic SNV discovery. How can I get the processed bam files? I know there is source code for MuTect at github, but I am not sure which java files are used in preprocessing steps. Can you please tell me the program files for low-quality reads preprocessing? Thanks very much for your time!