SomaticSniper (v1.0.5.0) ^[1]

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

Verscan

Installation

wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar

Usage

java -jar VarScan.jar  [COMMAND] [OPTIONS]

Prepare fasta to be used as reference genome

# Create fasta.dict
gatk CreateSequenceDictionary -R ref.fasta

# Create fasta.index
samtools faidx ref.fasta

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1. https://github.com/genome/somatic-sniper ↩︎