gnomad_qc.v4.create_release.make_var_annot_hists

usage: gnomad_qc.v4.create_release.make_var_annot_hists.py [-h]
                                                           [--determine_bounds]
                                                           [--data-type {exomes,genomes}]
                                                           [--test]

Named Arguments

--determine_bounds

Determine min/max values for each variant metric and prints them to stdout (to be used in hand-tooled histogram ranges). Note that this should only be run if the defaults do not result in well-behaved histograms.

Default: False

--data-type

Possible choices: exomes, genomes

Data type

Default: “exomes”

--test

Use test resources and test on PCSK9 region

Default: False

Module Functions

gnomad_qc.v4.create_release.make_var_annot_hists.LOG10_ANNOTATIONS	List of annotations to log scale when creating histograms.
gnomad_qc.v4.create_release.make_var_annot_hists.create_frequency_bins_expr_inbreeding(AF)	Create bins for frequencies in preparation for aggregating Inbreedind Coefficient by frequency bin.
gnomad_qc.v4.create_release.make_var_annot_hists.main(args)
gnomad_qc.v4.create_release.make_var_annot_hists.get_script_argument_parser()	Get script argument parser.

gnomad_qc.v4.create_release.make_var_annot_hists.LOG10_ANNOTATIONS = ['AS_VarDP', 'QUALapprox', 'AS_QUALapprox']

List of annotations to log scale when creating histograms.

gnomad_qc.v4.create_release.make_var_annot_hists.create_frequency_bins_expr_inbreeding(AF)

Create bins for frequencies in preparation for aggregating Inbreedind Coefficient by frequency bin.

Uses bins of < 0.0005 and >= 0.0005

NOTE: Frequencies should be frequencies from raw data. Used when creating site quality distribution json files.

Parameters:

AF (NumericExpression) – Field in input that contains the allele frequency information

Returns:

Expression containing bin name

Return type:

hl.expr.StringExpression

gnomad_qc.v4.create_release.make_var_annot_hists.main(args)