Bamsurgeon:

tools for adding mutations to .bam files, used for testing mutation callers

Please see doc/Manual.pdf for instructions and contact [email protected] with questions.

Installation

python setup.py build
python setup.py install

External Prerequisites:

The following presumes $HOME/bin is in your $PATH

Samtools / BCFTools / wgsim:

git clone https://github.com/samtools/htslib.git
make -C htslib

git clone https://github.com/samtools/samtools.git
make -C samtools
cp samtools/samtools $HOME/bin
cp samtools/misc/wgsim $HOME/bin

git clone https://github.com/samtools/bcftools.git
make -C bcftools
cp bcftools/bcftools $HOME/bin

BWA (or another aligner, currently supported aligners include bwa, novoalign, gsnap, bowtie2, and tmap)

git clone https://github.com/lh3/bwa.git
make -C bwa
cp bwa/bwa $HOME/bin

Picard tools

wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
unzip picard-tools-1.131.zip

Exonerate

git clone https://github.com/adamewing/exonerate.git
cd exonerate
git checkout v2.4.0
autoreconf -i
./configure && make && make check && make install

Velvet

wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar xvzf velvet_1.2.10.tgz
make -C velvet_1.2.10
cp velvet_1.2.10/velvetg $HOME/bin
cp velvet_1.2.10/velveth $HOME/bin

Pysam

pip install cython
pip install pysam