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?
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