Calculates the significance of seeing N de novo mutations with a summed severity in a given gene.
# you might need cython installed before this e.g. pip install cython
pip install git+git://github.com/jeremymcrae/severity_sampler.git --user
# Alternatively:
git clone https://github.com/jeremymcrae/severity_sampler.git
cd mupit
python setup.py install --user
python bin/simulate_severity.py \
--de-novos PATH_TO_DENOVOS \
--cadd PATH_TO_SNVS_CADD \
--constraint PATH_TO_REGIONAL_CONSTRAINT \
--cache CACHE_FOLDER \
--genome-build grch37 \
--output OUTPUT.txtCADD scores for SNVs are available from the CADD website (see file for all possible SNVs of GRCh37/hg19). Regional constraint scores are available for genes from Samocha et al., Table S2.