gnomad.resources.grch37.reference_data

`gnomad.resources.grch37.reference_data.get_truth_ht`()	Return a table with annotations from the latest version of the corresponding truth data.
`gnomad.resources.grch37.reference_data.transform_grch37_methylation`([...])	Transform methylation level from the GRCh37 methylation resource to a 0-2 scale.

gnomad.resources.grch37.reference_data.get_truth_ht()[source]

Return a table with annotations from the latest version of the corresponding truth data.

The following annotations are included:

hapmap
kgp_omni (1000 Genomes intersection Onni 2.5M array)
kgp_phase_1_hc (high confidence sites in 1000 genonmes)
mills (Mills & Devine indels)

Return type:: Table
Returns:: A table with the latest version of popular truth data annotations

gnomad.resources.grch37.reference_data.transform_grch37_methylation(ht=None, methylation_expr=None)[source]

Transform methylation level from the GRCh37 methylation resource to a 0-2 scale.

Note

One of ht or methylation_expr must be provided.

The GRCh37 methylation resource provides a MEAN score ranging from 0 to 1. We transform this to a 0-2 scale by converting any value greater than 0.6 to 2, any value less than or equal to 0.2 to 0, and any value in between to 1.

Parameters:

ht (Optional[Table]) – Optional Hail Table with methylation data. Default is None.
methylation_expr (Optional[NumericExpression]) – Optional methylation level expression. Default is None.

Return type:

Union[Table, NumericExpression]

Returns:

Transformed methylation level expression or annotated Hail Table.