SomaticSniper is a program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files).
- 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 28 (3): 311-317 (2012). doi:10.1093/bioinformatics/btr665
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>
-f option is required, where <ref.fasta> is a >REQUIRED reference sequence in the FASTA format