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Mutationseq

Install

  1. Create a directory to store temporary files:
     mkdir -p $HOME/museq/
     cd $HOME/museq
    
  2. Download and install Miniconda for python 2.7:

    Download miniconda

     wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
    

    Run

     sh Miniconda2-latest-Linux-x86_64.sh
    

    and follow the instructions. When you have finished following the instructions, you should have python installed:

     which python
     ~/miniconda2/bin/python
    
  3. clone the mutationseq repo.
     git clone -b easy_install https://dgrewal@svn.bcgsc.ca/bitbucket/scm/museq/mutationseq.git
    
  4. create a conda environment:
     conda create --name mutationseq python=2.7 --file $HOME/museq/mutationseq/conda_packages.txt
    
  5. activate the environment:
     conda activate mutationseq
    
  6. Install mutationseq:

    download boost:

     wget https://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.gz/download -O boost.tar.gz
    

    At the moment mutationseq only supports boost 1.57.0 or older. Newer versions will run into installation issues. extract boost:

     tar -xvf boost.tar.gz
    

    install mutationseq:

     cd $HOME/museq/mutationseq/
     python setup.py install --boost_source=$HOME/museq/boost_1_57_0
    

Running Mutationseq:

To call variants using MutationSeq, we use the following command:

mkdir -p museq/results; \
museq \
  normal:bam/HCC1395_exome_normal.sort.markdup.17.7MB-8MB.bam \
  tumour:bam/HCC1395_exome_tumour.sort.markdup.17.7MB-8MB.bam \
  reference:refs/GRCh37-lite.fa \
  -o museq/results/HCC1395_exome_tumour_normal_17.vcf