Reassign all mapping qualities above a certain value
I'm trying to do variant calling on RNA-seq data aligned with Tophat. I know that I need to use SplitNCigarReads, but I'm having some trouble reassigning mapping qualities. I can successfully reassign MQ of 255 as suggested in the best practices, but am still getting errors for MQ values that are above 60. Is there any way that I can reassign all mapping qualities above a certain value? It seems like there's only tools to do this for one specific MQ and not an entire range.