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identifying mutational significance in cancer genomes

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MuSiC2
===========
Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.

Usage
-----

Program:     music2 - Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.
    Version:     V0.2
    Author:      Beifang Niu && Matthew Wyczalkowski

Usage:  music2 <command> [options]

Key commands:

bmr                    ...  Calculate gene coverages and background mutation rates.
    smg                         Identify significantly mutated genes.
    long-gene-filter            Find conditions for which significance status is no longer related to gene size. 
    survival                    Create survival plots and P-values for clinical and mutational phenotypes.  
    clinical-correlation        Correlate phenotypic traits against mutated genes, or against individual variants.
    cosmic                      Match a list of variants to those in COSMIC, and highlight druggable targets.
    cosmic-omim                 Compare the amino acid changes of supplied mutations to COSMIC and OMIM databases.
    dendrix                     Discovery of mutated driver pathways in cancer using only mutation data. 
    dendri-permutation     ...  Run the permutation test for Dendrix. 
    mutation-relation           Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.
    path-scan                   Find signifcantly mutated pathways in a cohort given a list of somatic mutations.
    pfam                        Add Pfam annotation to a MAF file.
    proximity                   Perform a proximity analysis on a list of mutations.
    proximity-window            Perform a sliding window proximity analysis on a list of mutations.
    
    help      this message

Install (Ubuntu & CentOS)
-------
Note: We provided binaries for joinx, samtools, calcRoiCovg and bedtools in /bin dir, and which were compiled on CentOS, and tested on CentOS/Ubuntu.

Prerequisites for Ubuntu:

sudo apt-get install build-essential \
        git \
        cmake \
        curl \
        cpanminus
        libbz2-dev \
        libgtest-dev \
        libbam-dev \
        zlib1g-dev

Prerequisites for CentOS:

sudo yum install yum-utils
        sudo yum install curl
        sudo yum install git
        sudo yum install cmake
        sudo yum groupinstall "Development Tools"
        sudo yum update -y nss curl libcurl
        sudo yum install perl-devel
        sudo yum install perl-CPAN
        sudo yum install bzip2-libs
        sudo yum install zlib-devel
        sudo curl -L http://cpanmin.us | perl - --sudo App::cpanminus

Change C++11 compiler for CentOS (required for joinx installation)

Reference 
> https://www.softwarecollections.org/en/scls/rhscl/devtoolset-3/

1. Install a package with repository for your system:
    On CentOS, install package centos-release-scl available in CentOS repository:
        $ sudo yum install centos-release-scl
    On RHEL, enable RHSCL repository for you system:
        $ sudo yum-config-manager --enable rhel-server-rhscl-7-rpms
    2. Install the collection:
        $ sudo yum install devtoolset-3
    3. Start using software collections:
        $ scl enable devtoolset-3 bash
    Set env variables --optional
        CC=gcc CXX=g++

Install samtools ( Download the samtools-0.1.19 from SOURCEFORGE (http://sourceforge.net/projects/samtools/files/samtools/0.1.19) )

tar jxf samtools-0.1.19.tar.bz2
        cd samtools-0.1.19
        make
        export SAMTOOLS_DIR=$PWD
        sudo mv samtools /usr/local/bin/

Install calcRoiCovg

git clone https://github.com/Beifang/calcRoiCovg.git
        cd calc-roi-covg
        make
        sudo mv calcRoiCovg /usr/local/bin/

Install bedtools

wget https://github.com/arq5x/bedtools2/archive/v2.27.1.tar.gz
        tar -zxvf v2.27.1.tar.gz
        cd bedtools2-2.27.1/
        make
        sudo mv ./bin /usr/local/bin/

Install joinx

git clone --recursive https://github.com/genome/joinx.git
        cd joinx
        mkdir build
        cd build
        cmake ..
        make deps
        make
        sudo make install

Fix joinx bugs

StreamLineSource.cpp
        bool StreamLineSource::getline(std::string& line) {
            std::getline(_in, line);
            return true;
        }

Intall Perl modules

sudo cpanm Test::Most 
        sudo cpanm Statistics::Descriptive
        sudo cpanm Statistics::Distributions
        sudo cpanm Bit::Vector

Install MuSiC2 package
        
        git clone https://github.com/ding-lab/MuSiC2
        cd MuSiC2
        sudo cpanm MuSiC2-#.#.tar.gz

Notes: Python is needed to be installed if you run music2 dendrix & dendrix-permutation

example
-------

1. smg test example:

Make a dir for MuSiC2 smg running

mkdir music2_smg_running
        cd music2_smg_running

Make subdirs where all the runtime logs can be written

mkdir logs
        mkdir logs/calc_covg
 
Get calculate coverage command list

music2 bmr calc-covg --roi-file ./example/smg/example.roi_file --reference-sequence /reference_dir/ucsc.hg19.fa --bam-list ./example/smg/example.bam_list --output-dir . --cmd-list-file example.run-coverage-command

Run roi coverage for each sample

bash example.run-coverage-command

Run bmr calc-covg again to get gene coverage

music2 bmr calc-covg --roi-file ./example/smg/example.roi_file --reference-sequence /reference_dir/ucsc.hg19.fa --bam-list ./example/smg/example.bam_list --output-dir .

Run calc-bmr to measure overall and per-gene mutation rates. Give it extra memory, because it may need it

music2 bmr calc-bmr --roi-file ./example/smg/example.roi_file --reference-sequence /reference_dir/ucsc.hg19.fa --bam-list ./example/smg/example.bam_list --maf-file ./example/smg/example.input.maf --output-dir . --show-skipped

Run SMG test using an FDR threshold appropriate for these mutation rates

music2 smg --gene-mr-file gene_mrs --output-file smgs --max-fdr 0.05 --processors 1

2. dendrix example:

Runs the MCMC for 1000000 iterations, sampling sets of size 3 every 1000
iterations. Produces two files  (since 1 experiment is run):
        
        music2 dendrix --mutations-file example/dendrix/mutation_matrix --set-size 3 --minimum-freq 1 \
            --number-interations 1000000 --analyzed-genes-file example/dendrix/analyzed_genes \
            --number-experiments 1 --step-length 1000

If you want to compute the p-value for the second set having weight 47, you can run:
    
        music2 dendrix-permutation --mutations-file example/dendrix/mutation_matrix --set-size 3 --minimum-freq 1 \
            --number-interations 1000000 --analyzed-genes-file example/dendrix/analyzed_genes \
            --number-permutations 100 --value-tested 47 --rank 2

SUPPORT
-------

If you have any questions, please contact one or more of the following folks:

Beifang Niu <bniu@sccas.cn>
Li Ding <lding@wustl.edu>

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