Tools (addsnv.py, addindel.py and addsv.py) for adding genomic variants to SAM/BAM/CRAM files, used for testing variant callers
Please see doc/Manual.pdf for instructions and contact [email protected] with questions.
Before using simulation-based methods, consider whether there are validated benchmarking data available for your use case. For example the Genome in a Bottle or the PrecisionFDA Truth Challenge may provide a means to test on non-simulated data.
Bamsurgeon can be installed via bioconda: 
The following presumes $HOME/bin is in your $PATH
SAMtools / wgsim:
git clone --recurse-submodules --remote-submodules 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
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
git clone https://github.com/dzerbino/velvet.git
cd velvet
make
cp velvetg $HOME/bin
cp velveth $HOME/bin
Pysam
pip install pysam
To check if all dependencies are correctly installed, you may execute the following script:
python3 -O scripts/check_dependencies.py
Alternately, it is not necessary to install BAMSurgeon. It works as any other standalone Python script. Usage example:
python3 -O bin/addsv.py -p 1 -v test_data/test_sv.txt -f test_data/testregion_realign.bam -r test_data/Homo_sapiens_chr22_assembly19.fasta -o test_data/testregion_sv_mut.bam --aligner mem --keepsecondary --seed 1234 --inslib test_data/test_inslib.fa