Somatic Sniper
Here, we are learning how to use SomaticSniper to identify single nucleotide positions that are different between tumor and normal and further to filter variants using some provided Perl scripts [1] and bam-readcount [2].
1. SomaticSniper (v1.0.5.0) [3]
Purpose
SomaticSniper identifies single nucleotide positions that are different between tumor and normal.
Installation
# Build dependencies for Ubuntu
sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev
# Clone the git repo
git clone https://github.com/genome/somatic-sniper.git
# Build SomaticSniper
mkdir somatic-sniper/build
cd somatic-sniper/build
cmake ../
make deps
make -j
make test
# Add path to environment ~/.bashrc
export PATH=$PATH:/PATH_TO/somatic-sniper/build/bin
Usage
bam-somaticsniper [options] -f <ref.fasta> <tumor.bam> <normal.bam> <snv_output_file>
Recommended setting:
bam-somaticsniper -Q 40 -G -L -f reference.fa tumor.bam normal.bam output.txt
Recommended seeting by GR paper author: [4]
bam-somaticsniper -Q 40 -L -f reference.fa tumor.bam normal.bam output.txt
Parameters
-f FILE REQUIRED reference sequence in the FASTA format -Q INT filtering somatic snv output with somatic quality less than INT [15] -G FLAG do not report Gain of Referene variants as determined by genotypes -L FLAG do not report LOH variants as determined by genotypes
2. bam-readcount
TBA
3. Basic filtering with provided Perl scripts
A small number of basic Perl scripts are included in the SomaticSniper package (located in src/scripts of the source code release) [1:1] TBA