gnomad_qc.v5.annotations.annotation_utils

AoU-specific annotation utilities.

Module Functions

`gnomad_qc.v5.annotations.annotation_utils.annotate_adj`(mt)	Annotate genotypes with adj criteria.
`gnomad_qc.v5.annotations.annotation_utils.get_adj_expr`(...)	Get adj genotype annotation.

AoU-specific annotation utilities.

gnomad_qc.v5.annotations.annotation_utils.annotate_adj(mt, adj_gq=30, adj_ab=0.2)[source]

Annotate genotypes with adj criteria.

Defaults are similar to gnomAD values, but GQ >= 20 changed to GQ >= 30 to make up for lack of DP filter (raised GQ threshold to 30 to match DP 10 threshold in gnomAD defaults).

Parameters:

mt (MatrixTable) – Input MatrixTable.
adj_gq (int) – Minimum GQ. Default is 30.
adj_ab (float) – Minimum allele balance. Default is 0.2.

Return type:

MatrixTable

Returns:

MatrixTable with adj annotation.

gnomad_qc.v5.annotations.annotation_utils.get_adj_expr(gt_expr, gq_expr, ad_expr, adj_gq=30, adj_ab=0.2)[source]

Get adj genotype annotation.

Defaults are similar to gnomAD values, but GQ >= 20 changed to GQ >= 30 to make up for lack of DP filter.

Note

Assumes that the genotype expression is already adjusted for sex ploidy.

Parameters:

gt_expr (CallExpression) – Genotype expression.
gq_expr (Union[Int32Expression, Int64Expression]) – GQ expression.
ad_expr (ArrayNumericExpression) – Allele depth expression.
adj_gq (int) – Minimum GQ. Default is 30.
adj_ab (float) – Minimum allele balance. Default is 0.2.

Return type:

BooleanExpression

Returns:

Expression for adj genotype annotation.