Publication [Open access]

If you use SomaticSeq in your work, please cite the following:

  • Li Tai Fang, Pegah Tootoonchi Afshar, Aparna Chhibber, Marghoob Mohiyuddin, Yu Fan, John C. Mu, Greg Gibeling, Sharon Barr, Narges Bani Asadi, Mark B. Gerstein, Daniel C. Koboldt, Wenyi Wang, Wing H. Wong, and Hugo Y.K. Lam. An Ensemble Approach to Accurately Detect Somatic Mutations Using SomaticSeq. Genome Biology, 16(1):197. (2015). DOI: 10.1186/s13059-015-0758-2

SomaticSeq placed #1 and #2 in INDEL and SNV in the Stage 5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge.

Watch the quick 8-minute youtube video describing SomaticSeq, or the SomaticSeq Webinar On Demand.

Documentation can be directly downloaded here.

Data used in the manuscript is described here.

Download SomaticSeq

Software Dependencies

Running SomaticSeq

This SomaticSeq workflow takes about 3 hours for an ensmeble call set of 50K calls. You may use the script or create your own pipeline script. The shell command (All VCF files need to be properly sorted. VCF files can also be bgzipped, but make sure they have .gz extension).
Long options shown here are only available for v2.0.3 or later.

Command-line options for

Long options only available after v2.0.3

Contact Us

Please report bugs and suggestions to the report issues page. The developers will be notified immediately. Alternatively, you may email


A short video describing SomaticSeq: