package varspark.hail

This package contains variant spark integration with Hail.

import hail as hl
import varspark.hail as vshl
vshl.init()
vds = hl.import_vcf(...)
...

rf_model = vshl.random_forest_model(y=vds.label,
            x=vds.GT.n_alt_alleles(), seed = 13, mtry_fraction = 0.05,
            min_node_size = 5, max_depth = 10)
rf_model.fit_trees(100, 50)
impTable = rf_model.variable_importance()
rf_model.release()

module varspark.hail.rf

module varspark.hail.plot