Mutationseq

Install

Create a directory to store temporary files:
```
mkdir -p $HOME/museq/
cd $HOME/museq
```
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
```

clone the mutationseq repo.

git clone https://github.com/shahcompbio/mutationseq.git

create a conda environment:

conda create --name mutationseq python=2.7 --file $HOME/museq/mutationseq/conda_packages.txt

activate the environment:
```
conda activate mutationseq
```

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