Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.


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

Installed on blacklight.

Other resources that may be helpful include:

  • 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

Running SomaticSniper

On blacklight

SomaticSniper is available for use through the module command. To load the SomaticSniper module enter:

module load SomaticSniper

General Usage

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


Required options

The -f option is required:

-f FILE REQUIRED reference sequence in the FASTA format


Other options

-F STRING select output format [classic]
Available formats:
  • classic
  • vcf
  • bed
-J FLAG Use prior probabilities accounting for the somatic mutation rate
-N INT number of haplotypes in the sample (for -c/-g) [2]
-n STRING normal sample id (for VCF header) [NORMAL]
-p FLAG disable priors in the somatic calculation. Increases sensitivity for solid tumors
-Q INT filtering somatic snv output with somatic quality less than INT [15]
-q INT filtering reads with mapping quality less than INT [0]
-r FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]
-s FLOAT prior probability of a somatic mutation (implies -J) [0.010000]
-T FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]
-t STRING tumor sample id (for VCF header) [TUMOR]
-v Display version information