The latest release of SomaticSniper, The Genome Institute’s somatic SNV calling workhorse, adds an alternative statistical model that better accounts for the rarity of somatic events by jointly considering the tumor and normal genotypes. This version also adds native support for the VCF and BED formats as output. The VCF output contains information useful for downstream filtering, e. g., fraction of reads on the forward and reverse strands, average read mapping quality, and average base quality for reads/bases supporting the variant allele and those supporting the reference allele.

You can download this release on Github.