16 months ago by
Washington University in St. Louis, MO
It just depends on what you're doing. Somatic Sniper has largely been superceded by a new generation of callers (Mutect, Strelka, etc) but is still useful in the niche case of having tumor contamination in your normal sample (very few other callers are designed to handle this case). In general, VarScan has kept up with the times pretty well.
That said, relying on a single caller is probably not your best bet. Each has strengths and weaknesses, and an ensemble approach followed by intelligent merging is probably your best bet for maximizing your performance.