Download and Install

Install using pip

sudo pip install transvar

or locally

pip install --user transvar

to upgrade from a previous version

pip install -U transvar

Try out the docker image

Also try out using the pre-built docker image Assuming the existence of ~/references/hg38/hg38.fa and ~/references/hg38/hg38.fa.fai

docker pull zhouwanding/transvar:2.4.6
docker run -v ~/references/hg38:/data -ti zhouwanding/transvar:2.4.6 transvar panno -i PIK3CA:p.E545K --ensembl --reference /data/hg38.fa

Download the program

Current release

Latest release is available here

For all previous versions, see here

Other old stable releases


The only requirement for building TransVar are Python 2.7 and a reasonably modern C compiler such as gcc.

Install from source

Local install

python install --prefix [folder]

The installation will create two subfolders: [folder]/lib (which would contain libraries) and [folder]/bin (which would contain transvar executable).

When you run transvar, make sure [folder]/lib/python2.7/site-packages is in your PYTHONPATH. In some occasions, you need to mkdir -p [folder]/lib/python2.7/site-packages to make sure it exists before you could run You can add it by putting

export PYTHONPATH=$PYTHONPATH:[folder]/lib/python-2.7/site-packages/

to your .bashrc or .profile depending on your OS.

The installed executable is [folder]/bin/transvar.

System-wise install (need root)

sudo python install