<commit_before>.. image:: https://raw.githubusercontent.com/apriha/lineage/master/docs/images/lineage_banner.png

|build| |codecov| |docs| |pypi| |python| |downloads| |license|

lineage
=======
``lineage`` provides a framework for analyzing genotype (raw data) files from direct-to-consumer
(DTC) DNA testing companies, primarily for the purposes of genetic genealogy.

Capabilities
------------
- Compute centiMorgans (cMs) of shared DNA between individuals using the HapMap Phase II genetic map
- Plot shared DNA between individuals
- Determine genes shared between individuals (i.e., genes transcribed from shared DNA segments)
- Find discordant SNPs between child and parent(s)
- Read, write, merge, and remaps SNPs for an individual via the  `snps <https://github.com/apriha/snps>`_ package

Supported Genotype Files
------------------------
``lineage`` supports `VCF <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/>`_ files and
genotype files from the following DTC DNA testing companies:

- `23andMe <https://www.23andme.com>`_
- `Ancestry <https://www.ancestry.com>`_
- `Family Tree DNA <https://www.familytreedna.com>`_
- `MyHeritage <https://www.myheritage.com>`_

Dependencies
------------
``lineage`` requires `Python <https://www.python.org>`_ 3.5+ and the following Python packages:

- `numpy <http://www.numpy.org>`_
- `pandas <http://pandas.pydata.org>`_
- `matplotlib <http://matplotlib.org>`_
- `atomicwrites <https://github.com/untitaker/python-atomicwrites>`_
- `snps <https://github.com/apriha/snps>`_

On Linux systems, the following system-level installs may also be required::
<commit_msg>Update supported genotype files note<commit_after>.. image:: https://raw.githubusercontent.com/apriha/lineage/master/docs/images/lineage_banner.png

|build| |codecov| |docs| |pypi| |python| |downloads| |license|

lineage
=======
``lineage`` provides a framework for analyzing genotype (raw data) files from direct-to-consumer
(DTC) DNA testing companies, primarily for the purposes of genetic genealogy.

Capabilities
------------
- Compute centiMorgans (cMs) of shared DNA between individuals using the HapMap Phase II genetic map
- Plot shared DNA between individuals
- Determine genes shared between individuals (i.e., genes transcribed from shared DNA segments)
- Find discordant SNPs between child and parent(s)
- Read, write, merge, and remaps SNPs for an individual via the  `snps <https://github.com/apriha/snps>`_ package

Supported Genotype Files
------------------------
``lineage`` supports all genotype files supported by `snps <https://github.com/apriha/snps>`_.

Dependencies
------------
``lineage`` requires `Python <https://www.python.org>`_ 3.5+ and the following Python packages:

- `numpy <http://www.numpy.org>`_
- `pandas <http://pandas.pydata.org>`_
- `matplotlib <http://matplotlib.org>`_
- `atomicwrites <https://github.com/untitaker/python-atomicwrites>`_
- `snps <https://github.com/apriha/snps>`_

On Linux systems, the following system-level installs may also be required::

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