variant_annotation

gentropy.variant_annotation.VariantAnnotationStep

Variant annotation step.

Variant annotation step produces a dataset of the type VariantAnnotation derived from gnomADs gnomad.genomes.vX.X.X.sites.ht Hail's table. This dataset is used to validate variants and as a source of annotation.

Source code in src/gentropy/variant_annotation.py

class VariantAnnotationStep:
    """Variant annotation step.

    Variant annotation step produces a dataset of the type `VariantAnnotation` derived from gnomADs `gnomad.genomes.vX.X.X.sites.ht` Hail's table. This dataset is used to validate variants and as a source of annotation.
    """

    def __init__(self, session: Session, variant_annotation_path: str) -> None:
        """Run Variant Annotation step.

        Args:
            session (Session): Session object.
            variant_annotation_path (str): Variant annotation dataset path.
        """
        # Initialise hail session.
        hl.init(sc=session.spark.sparkContext, log="/dev/null")
        # Run variant annotation.
        variant_annotation = GnomADVariants().as_variant_annotation()
        # Write data partitioned by chromosome and position.
        (
            variant_annotation.df.write.mode(session.write_mode).parquet(
                variant_annotation_path
            )
        )

__init__(session: Session, variant_annotation_path: str) -> None

Run Variant Annotation step.

Parameters:

Name	Type	Description	Default
session	Session	Session object.	required
variant_annotation_path	str	Variant annotation dataset path.	required

Source code in src/gentropy/variant_annotation.py

def __init__(self, session: Session, variant_annotation_path: str) -> None:
    """Run Variant Annotation step.

    Args:
        session (Session): Session object.
        variant_annotation_path (str): Variant annotation dataset path.
    """
    # Initialise hail session.
    hl.init(sc=session.spark.sparkContext, log="/dev/null")
    # Run variant annotation.
    variant_annotation = GnomADVariants().as_variant_annotation()
    # Write data partitioned by chromosome and position.
    (
        variant_annotation.df.write.mode(session.write_mode).parquet(
            variant_annotation_path
        )
    )

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• 2023-01-15
• 2024-01-18
• Contributors