UniversalSNPsplit is an universal solution for splitting reads from bam file based on list of SNPs. The splitting is independent of the feature of reads alignment, such as mismatch, indel, splicing and pair-end. The splitting is also independent of library type, for example, RNA-seq, Chip-seq, WGBS and Hi-C. It is the most sensitive software so far for the same purpose.
UniversalSNPsplit can also be run in a parallel computing mode which makes it super fast.