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 

Running VarScan

1) Make SomaticSniper availiable for use

a) 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:


Last Updated on Saturday, 09 November 2013 10:41  

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