VariantDataset

class hail.vds.VariantDataset

Class for representing cohort-level genomic data.

This class facilitates a sparse, split representation of genomic data in which reference block data and variant data are contained in separate MatrixTable objects.

Parameters

• reference_data (MatrixTable) – MatrixTable containing only reference block data.

• variant_data (MatrixTable) – MatrixTable containing only variant data.

Attributes

reference_genome

Dataset reference genome.

Methods

checkpoint	Write to path and then read from path.
from_merged_representation	Create a VariantDataset from a sparse MatrixTable containing variant and reference data.
n_samples	The number of samples present.
validate	Eagerly checks necessary representational properties of the VDS.
write	Write to path.

checkpoint(path, **kwargs)

Write to path and then read from path.

static from_merged_representation(mt, *, ref_block_fields=(), infer_ref_block_fields=True)

Create a VariantDataset from a sparse MatrixTable containing variant and reference data.

n_samples()

The number of samples present.

property reference_genome

Dataset reference genome.

Returns

ReferenceGenome

validate(*, check_data=True)

Eagerly checks necessary representational properties of the VDS.

write(path, **kwargs)

Write to path.