Genetics
--------

.. _methods_genetics:

.. currentmodule:: hail.methods

.. toctree::
    :maxdepth: 2

.. autosummary::

    VEPConfig
    VEPConfigGRCh37Version85
    VEPConfigGRCh38Version95
    balding_nichols_model
    concordance
    filter_intervals
    filter_alleles
    filter_alleles_hts
    hwe_normalized_pca
    genetic_relatedness_matrix
    realized_relationship_matrix
    impute_sex
    ld_matrix
    ld_prune
    compute_charr
    mendel_errors
    de_novo
    nirvana
    sample_qc
    _logistic_skat
    skat
    lambda_gc
    split_multi
    split_multi_hts
    summarize_variants
    transmission_disequilibrium_test
    trio_matrix
    variant_qc
    vep

.. autoclass:: VEPConfig
.. autoclass:: VEPConfigGRCh37Version85
.. autoclass:: VEPConfigGRCh38Version95

.. autofunction:: balding_nichols_model
.. autofunction:: concordance
.. autofunction:: filter_intervals
.. autofunction:: filter_alleles
.. autofunction:: filter_alleles_hts
.. autofunction:: hwe_normalized_pca
.. autofunction:: genetic_relatedness_matrix
.. autofunction:: realized_relationship_matrix
.. autofunction:: impute_sex
.. autofunction:: ld_matrix
.. autofunction:: ld_prune
.. autofunction:: compute_charr
.. autofunction:: mendel_errors
.. autofunction:: de_novo
.. autofunction:: nirvana
.. autofunction:: sample_qc
.. autofunction:: _logistic_skat
.. autofunction:: skat
.. autofunction:: lambda_gc
.. autofunction:: split_multi
.. autofunction:: split_multi_hts
.. autofunction:: summarize_variants
.. autofunction:: transmission_disequilibrium_test
.. autofunction:: trio_matrix
.. autofunction:: variant_qc
.. autofunction:: vep