gnomad_qc.v4.annotations.generate_freq_genomes
==============================================


Script to create frequencies HT for v4.0 genomes.

This script is written specifically for the v4.0 genomes release to handle the
addition and subtraction of samples from the HGDP + 1KG subset. The HGDP + 1KG
subset has updated sample QC annotations. The addition of new samples from the
densified MT will include new variants, which will require the recomputation of AN
for the v3.1 releases samples, and merging it to call stats of the v3.1.2 release
sites HT and of updated HGDP + 1KG subset. In addition, the code will also get the
other call stats related annotations, including: filtering allele frequencies ('faf'),
'grpmax', 'gen_anc_faf_max' and 'InbreedingCoeff' as done in v4.0 exomes.





.. argparse::
   :ref: gnomad_qc.v4.annotations.generate_freq_genomes.get_script_argument_parser
   :prog: gnomad_qc.v4.annotations.generate_freq_genomes.py



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

.. gnomad_automodulesummary:: gnomad_qc.v4.annotations.generate_freq_genomes

.. automodule:: gnomad_qc.v4.annotations.generate_freq_genomes
    :exclude-members: get_script_argument_parser