postVEP

The Python package helps you analyze Variant Effect Predictor (VEP) result.

Prerequisite

• Python 3

Installation

pip install .

Quick start

from postVEP import VEPresult
r = VEPresult('./example/output_with_plugin.tsv') # r.data is a pandas DataFrame
print(r.get_all_col_names())
print(r.get_missing_cols())
print(r.get_col_info('gnomAD_exomes_ASJ_AF'))
print(r.get_col_by_name('Allele'))
print(r.get_LD_col('LinkedVariants_CHS'))

To learn more, check our tutorial in Jupyter Notebook

Report issuse

https://github.com/PittGenomics/postVEP/issues