Fork me on GitHub!



  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




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

     which python
  3. clone the mutationseq repo.
     git clone -b easy_install
  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 -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 $HOME/museq/mutationseq/
     python install --boost_source=$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