simGL
=====

**simGL** simulates genotype likelihoods (GLs) from haplotypic genotype matrices,
given information about per-sample coverage and sequencing error rates.
It is designed to work seamlessly with the output of
`tskit <https://tskit.dev>`_ and `msprime <https://tskit.dev/msprime/>`_
in Python pipelines, but can be used with any haplotypic genotype matrix.

.. toctree::
   :maxdepth: 2
   :caption: Contents

   installation
   quickstart
   userguide
   theory
   API Reference <autoapi/index>
   citation
   changelog

Indices and tables
------------------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`