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 was the tool that had Bina Technologies, Inc. ranked #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.

Documentation can be directly downloaded here.

Download SomaticSeq

Software Dependencies

Running SomaticSeq

Example command to merge caller results and extract SomaticSeq features

Tumor-normal paired mode

Tumor-only single mode

Additional parameters to be specified before paired or single option to invoke training mode.

Additional input files to be specified before paired or single option invoke prediction mode (to use classifiers to score variants)


A short video describing SomaticSeq:

Contact Us

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