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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




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.