ding-lab / music2

identifying mutational significance in cancer genomes

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 [email protected] Li Ding [email protected]