To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

MuTect with RADseq data - disabling strand bias and clustered position filters

Liz10683Liz10683 United StatesMember

I would like to analyze a dataset consisting of RADseq (Restriction-site Associated DNA) tags from tumor and normal samples. By nature of the technique, all of 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?

Sign In or Register to comment.