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SomaticSeq is a flexible post-somatic-mutation-calling workflow for improved accuracy. It has incorporated multiple somatic mutation caller(s) to obtain a combined call set, and then it uses machine learning to distinguish true mutations from false positives from that call set. It has incorporated the following somatic mutation callers:

  • MuTect/Indelocator/MuTect2,
  • VarScan2,
  • JointSNVMix,
  • SomaticSniper,
  • VarDict,
  • MuSE,
  • LoFreq,
  • Scalpel,
  • Strelka, and
  • TNscope


MetaCentrum provides following modules:

  • somaticseq-2.7.0 (released: December 2017), NOTE: This module does not load any version of R programming language - if you want to use this language,
    you will need to load a module on your own


SomaticSeq is a "wrapper" which "puts together" a lot of other programs. Here you can find out, what exactly are SomaticSeq modules composed of.

Version somaticseq-2.7.0

SomaticSeq currently supports about 9 somatic mutation callers. In majority of cases, these callers are installed beside SomaticSeq (the only exception is Mutect2, which is in totally different module):

  1. Mutect2 - part of the GATK 4 toolkit (which gets loaded automatically with the SomaticSeq module)
  2. VarScan2 - convenience wrapper script available, so after module load somaticseq-2.7.0, you can execute varscan and help will be printed.
    The wrapper script works like this: java -jar /software/somaticseq/2.7.0/VarScan/varscan.jar "$@"
  3. JointSNVMix2 - you can run this caller simply by executing the command. You can try -h train or -h classify to get help...
  4. SomaticSniper - run any of the scripts directly, for example --help
  5. VarDict - run any of the scripts directly, for example -h or -h
  6. MuSE - run MuSE <command> [options]
  7. LoFreq - run lofreq, or any other caller's script
  8. Scalpel - run scalpel-discovery, scalpel-export, or any other caller's script
  9. Strelka2 - run strelka2 or other caller's script


BSD 2-Clause "Simplified" License


Warning.gif TODO: Write this section after app gets installed & tested!


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


Official Manual.pdf

Program administrator