Skip to content
identifying mutational significance in cancer genomes
Branch: master
Clone or download
Beifang Merge pull request #12 from niu-lab/master
dendrix running example added
Latest commit bd577fd Dec 3, 2018
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
bin remove modules not ready Sep 13, 2018
example add smg test commands example Nov 23, 2018
lib/TGI/MuSiC2 dendrix running example added Dec 3, 2018
t Clinical Correlation preliminary implementation Feb 9, 2017
LICENSE.md add MIT License Nov 10, 2017
MuSiC2-0.2.tar.gz
README.md
dist.ini Documentation update Feb 8, 2017

README.md

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 && Cyriac Kandoth && 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
  1. 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 Cyriac Kandoth ckandoth@gmail.com Li Ding lding@wustl.edu

You can’t perform that action at this time.