Annotation

Annotations are Hail’s way of adding data fields to Hail’s tables and matrix tables.

Create a nested annotation

description:

Add a new field gq_mean as a nested field inside info

code:

>>> mt = mt.annotate_rows(info=mt.info.annotate(gq_mean=hl.agg.mean(mt.GQ)))

dependencies:

StructExpression.annotate(), MatrixTable.annotate_rows()

understanding:

To add a new field gq_mean as a nested field inside info, instead of a top-level field, we need to annotate the info field itself.

Construct an expression mt.info.annotate(gq_mean=...) which adds the field to info. Then, reassign this expression to info using MatrixTable.annotate_rows().

Remove a nested annotation

description:

Drop a field AF, which is nested inside the info field.

To drop a nested field AF, construct an expression mt.info.drop('AF') which drops the field from its parent field, info. Then, reassign this expression to info using MatrixTable.annotate_rows().

code:

>>> mt = mt.annotate_rows(info=mt.info.drop('AF'))

dependencies:

StructExpression.drop(), MatrixTable.annotate_rows()