Pittsburgh Supercomputing Center 

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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)

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 Bioinformatics (2012) 28 (3): 311-317 doi:10.1093/bioinformatics/btr665

Running VarScan

  1. Make SomaticSniper availiable for use
    1. On blacklight:
      SomaticSniper will be made availiable for use through the module command. To load the SomaticSniper module enter:
      module load SomaticSniper
  2. General Usage:
    bam-somaticsniper [options] -f <ref.fasta> <tumor.bam> <normal.bam> <snp_output_file>

    Required Option:

    -f FILE REQUIRED reference sequence in the FASTA format


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

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