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SomaticSniper is a program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files).


  • http://gmt.genome.wustl.edu/somatic-sniper
  • David E. Larson,Christopher C. Harris,Ken Chen,Daniel C. Koboldt, Travis E. Abbott,David J. Dooling,Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, and Li Ding SomaticSniper: identification of somatic point mutations in whole genome sequencing data Bioinformatic28 (3): 311-317 (2012).  doi:10.1093/bioinformatics/btr665



  • Bridges

  • BioU


To see what other modules are needed, what commands are available and how to get additional help type

module help somaticsniper


To see what versions of SomaticSniper are available type

module avail somaticsniper


To use SomaticSniper, include a command like this in your batch script to load the SomaticSniper module:

module load somaticsniper

Be sure you also load any other modules needed, as listed by the module help somaticsniper command.


The general form of the somatic-sniper command line is

bam-somaticsniper [options] -f <ref.fasta> <tumor.bam> <normal.bam> <snp_output_file>

The -f option is required, where <ref.fasta> is a >REQUIRED reference sequence in the FASTA format


See more help on SomaticSniper.