Varfilter filters variants based on quality filters. Various filters can be used: RMS mapping quality for gaps, read depth, SNP quality, indel quality, etc.
Parent program: samtools
SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. It is very convinient for handling reads mapped to reference genome. Normally SAMtools is used in intermediate step between raw read mapping and SNP or variants callingm, because it allows to effeciently store mapped reads.