MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

1.download MatlabMCR

mkdir -p app/MatlabMCR
cd app/MatlabMCR

wget -c http://ssd.mathworks.com/supportfiles/downloads/R2016a/deployment_files/R2016a/installers/glnxa64/MCR_R2016a_glnxa64_installer.zip

unzip MCR_R2016a_glnxa64_installer.zip
./install -mode silent -agreeToLicense yes -destinationFolder 
~/app/MatlabMCR

LD_LIBRARY_PATH="~/app/MatlabMCR/v901/runtime/glnxa64:~/app/MatlabMCR/v901/bin/glnxa64:~/app/MatlabMCR/v901/sys/os/glnxa64:~/app/MatlabMCR/v901/sys/opengl/lib/glnxa64"

2. download MutSigCV

cd ~/app
wget -c https://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSigCV_1.41.zip
unzip MutSigCV_1.41.zip

install MutSigCV

cd ~/app/MutSigCV_1.41/
mkdir req_files
cd req_files
wget -c http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/reference_files/gene.covariates.txt
wget -c http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/reference_files/exome_full192.coverage.zip
wget -c http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/reference_files/mutation_type_dictionary_file.txt

3. use MutSigCV

cd ~/app/MutSigCV_1.41/req_files
bash ../run_MutSigCV.sh  \
~/app/MatlabMCR/v901/ \
UCEC_mutect_mutsig_corrected.maf \
exome_full192.coverage.txt \
gene.covariates.txt \
mutsig_out_ \
mutation_type_dictionary_file.txt \
chr_files_hg38.txt

reference software.broadinstitute.org/cancer/cga/mutsig