The SomaticSniper whole exome variant caller was one of the first generation somatic mutation callers developed by the scientific community. It works the best with blood cancer that has high level of tumor-in-normal contaminations, but is often overly permissive for solid tumors. Since our first data release in 2016, the GDC has gradually adopted newer tools or new tool versions, and has transited the focus of somatic variant calling from any single caller to multi-caller ensemble.
After comparing ensemble calls with and without SomaticSniper and also receiving feedback from the authors of SomaticSniper, the GDC decided to remove this tool from our production in Data Release 35. The GDC still maintains other four whole exome variant callers, including MuSE, MuTect2, Pindel, and VarScan2.