gnomad_qc.v5.annotations.generate_frequency
===========================================


Script to generate frequency data for gnomAD v5.

This script calculates variant frequencies and histograms for:
1. gnomAD dataset - updating v4 frequencies by subtracting consent withdrawal samples
2. AoU dataset - using either pre-computed allele numbers or a densify approach

Processing Workflow:
--------------------
gnomAD (--process-gnomad):
1. Load v4 frequency table (contains frequencies and age histograms)
2. Prepare consent withdrawal VDS (split multiallelics, annotate metadata)
3. Calculate frequencies and age histograms for consent samples
4. Subtract from v4 frequencies to get updated gnomAD v5 frequencies

AoU (--process-aou):
1. Load AoU VDS with metadata
2. Prepare VDS (annotate group membership, adjust for ploidy, split multi-allelics)
3. Calculate frequencies using either: All sites ANs (efficient, requires pre-computed
AN values) or Densify approach (standard, more resource intensive)
4. Generate age histograms during frequency calculation

Usage Examples:
---------------
# Process AoU dataset using all-sites ANs.
python generate_frequency.py --process-aou --use-all-sites-ans --environment rwb

# Process AoU on batch/QoB with custom resources.
python generate_frequency.py --process-aou --environment batch --app-name "aou_freq" --driver-cores 8 --worker-memory highmem

# Process gnomAD consent withdrawals
python generate_frequency.py --process-gnomad --environment dataproc

# Run gnomAD in test mode
python generate_frequency.py --process-gnomad --test --test-partitions 2





.. argparse::
   :ref: gnomad_qc.v5.annotations.generate_frequency.get_script_argument_parser
   :prog: gnomad_qc.v5.annotations.generate_frequency.py



Module Functions
****************

.. gnomad_automodulesummary:: gnomad_qc.v5.annotations.generate_frequency

.. automodule:: gnomad_qc.v5.annotations.generate_frequency
    :exclude-members: get_script_argument_parser