SomaticSeq

Description

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

Availability

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

Components

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 jsm.py command. You can try jsm.py -h train or jsm.py -h classify to get help...
4. SomaticSniper - run any of the scripts directly, for example fpfilter.pl --help
5. VarDict - run any of the scripts directly, for example minivardict.sh -h or var2vcf_paired.pl -h
6. MuSE - run MuSE <command> [options]
7. LoFreq - run lofreq, lofreq2_somatic.py or any other caller's script
8. Scalpel - run scalpel-discovery, scalpel-export, FindVariants.pl or any other caller's script
9. Strelka2 - run strelka2 or other caller's script

License

BSD 2-Clause "Simplified" License

Usage

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

Citation

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

Documentation

Official Manual.pdf

Homepage

bioinform.github.io/somaticseq