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Variant Effect Prediction for Python

Project description

WARNING: This code is an alpha release and not production-ready. APIs may change at any time.

Veppy is a genetic variant effect predictor for Python. Inspired by SnpEff and VEP.


$ pip install veppy

Installation from source

$ git clone
$ cd veppy
$ python install


Step 1 (OPTIONAL): Prepare a directory for veppy data

The default data path is: ./data

You can override this by setting $VEPPY_DATA_DIR.

export VEPPY_DATA_DIR=/opt/veppy

Step 2: Download source data and build indexes

NOTE: This step downloads about 1gb of data. After indexing, the data directory will consume about 8gb of disk space.


Step 3: Index the source data

python ./

Example Usage

>>> from veppy.veppy import calculate_consequences
>>> variant = ('1', 8025384, 'A', 'T')
>>> result = calculate_consequences('GRCh37', *variant)
>>> print result.results


Tests are currently based on chr1 versions of input data. Full genome tests are coming soon!

$ nosetests


$ nosetests --with-coverage --cover-package=veppy

About SolveBio

SolveBio is a genomics company based in New York City.

Project details

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