ld_index

gentropy.ld_index.LDIndexStep

LD index step.

This step is resource intensive

Suggested params: high memory machine, 5TB of boot disk, no SSDs.

Source code in src/gentropy/ld_index.py

class LDIndexStep:
    """LD index step.

    !!! warning "This step is resource intensive"

        Suggested params: high memory machine, 5TB of boot disk, no SSDs.
    """

    def __init__(self, session: Session, min_r2: float, ld_index_out: str) -> None:
        """Run step.

        Args:
            session (Session): Session object.
            min_r2 (float): Minimum r2 to consider when considering variants within a window.
            ld_index_out (str): Output LD index path.
        """
        hl.init(sc=session.spark.sparkContext, log="/dev/null")
        (
            GnomADLDMatrix()
            .as_ld_index(min_r2)
            .df.write.partitionBy("chromosome")
            .mode(session.write_mode)
            .parquet(ld_index_out)
        )
        session.logger.info(ld_index_out)

__init__(session: Session, min_r2: float, ld_index_out: str) -> None

Run step.

Parameters:

Name	Type	Description	Default
session	Session	Session object.	required
min_r2	float	Minimum r2 to consider when considering variants within a window.	required
ld_index_out	str	Output LD index path.	required

Source code in src/gentropy/ld_index.py

def __init__(self, session: Session, min_r2: float, ld_index_out: str) -> None:
    """Run step.

    Args:
        session (Session): Session object.
        min_r2 (float): Minimum r2 to consider when considering variants within a window.
        ld_index_out (str): Output LD index path.
    """
    hl.init(sc=session.spark.sparkContext, log="/dev/null")
    (
        GnomADLDMatrix()
        .as_ld_index(min_r2)
        .df.write.partitionBy("chromosome")
        .mode(session.write_mode)
        .parquet(ld_index_out)
    )
    session.logger.info(ld_index_out)

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• 2023-03-10
• 2024-01-18
• Contributors