gnomad_qc.v4.assessment.calculate_per_sample_stats
==================================================


Script to get per-sample variant counts and aggregate sample statistics.

The following per-sample variant counts (including heterozygous, homozygous, non-ref, singletons etc.) can be calculated:

    - Total number of variants
    - Number of variants that pass all variant qc filters
    - Number of variants in UK Biobank capture regions
    - Number of variants in Broad capture regions
    - Number of variants in the intersect of UK Biobank and Broad capture regions
    - Number of variants in the union of UK Biobank and Broad capture regions
    - Number of rare variants (adj AF <0.1%)
    - Number of loss-of-function variants
    - Number of missense variants
    - Number of synonymous variants

The following aggregate sample stats of all of the above per-sample counts can be
computed:

        - Mean
        - Quantiles (0.0, 0.25, 0.5, 0.75, 1.0)

Aggregated statistics can also be computed by ancestry.






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

.. gnomad_automodulesummary:: gnomad_qc.v4.assessment.calculate_per_sample_stats

.. automodule:: gnomad_qc.v4.assessment.calculate_per_sample_stats
    :exclude-members: get_script_argument_parser