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.
disable strand bias and clustered position filters, mutect
Hi, I would like to analyze a dataset consisting of RADseq (Restriction-site Associated DNA) tags from tumor and normal samples. With Radseq, the reads start at restriction enzyme cut sites in the genome - therefore the assumptions that mutations will be covered by reads from both directions and staggered with respect to position in the read are violated. Is there a way to override the strand bias and clustered position filters in the MuTect pipeline?