The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.

This tool is developed by David E. Larson etc.

References:

• https://academic.oup.com/bioinformatics/article/28/3/311/188933

• http://gmt.genome.wustl.edu/packages/somatic-sniper/

• Module Name: somaticsniper (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load somaticsniper
[user@cn3144 ~]$ bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load somaticsniper
bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile
cd dir2; bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile
cd dir3; bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile
cd dir4; bam-somaticsniper -f ref.fasta tumor.bam normal.bam Outfile

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module somaticsniper