.. _seg_prob_file_format:

Segregation file
================

Input file
~~~~~~~~~~

Input for hybrid mode imputation. Same format as the output.

Output file
~~~~~~~~~~~

The ``.seg_prob.txt`` file contains *segregation probabilities* for each individual.
There are four lines per individual,
corresponding to the four possible patterns of segregation (inheritance):

  1. The grand *paternal* allele from the father and
     the grand *paternal* allele from the mother: :math:`Pr(F_{p,-} \& M_{p,-})`,
  2. The grand *paternal* allele from the father and
     the grand *maternal* allele from the mother: :math:`Pr(F_{p,-} \& M_{-,m})`,
  3. The grand *maternal* allele from the father and
     the grand *paternal* allele from the mother: :math:`Pr(F_{-,m} \& M_{p,-})`, and
  4. The grand *maternal* allele from the father and
     the grand *maternal* allele from the mother: :math:`Pr(F_{-,m} \& M_{-,m})`.

The symbols above mean the following:
``Pr()`` probability,
``F`` father,
``M`` mother,
``p`` *paternal* allele,
``m`` *maternal* allele, and
``-`` the allele that was not inherited.

.. TODO: Do we need a diagram for this maybe even show the 4 cases so we bring home the message!?

The first value in each line is the individual ID.
The remaining values are segregation probabilities at each locus.

Example with four individuals and four loci:

::

  id1 0.2500 0.2500 0.2500 0.2500
  id1 0.2500 0.2500 0.2500 0.2500
  id1 0.2500 0.2500 0.2500 0.2500
  id1 0.2500 0.2500 0.2500 0.2500
  id2 0.2500 0.2500 0.2500 0.2500
  id2 0.2500 0.2500 0.2500 0.2500
  id2 0.2500 0.2500 0.2500 0.2500
  id2 0.2500 0.2500 0.2500 0.2500
  id3 0.3356 0.3894 0.5000 0.4390
  id3 0.1644 0.1106 0.0000 0.0610
  id3 0.3356 0.3894 0.5000 0.4390
  id3 0.1644 0.1106 0.0000 0.0610
  id4 0.2046 0.1953 0.2760 0.3914
  id4 0.2954 0.3047 0.2240 0.1086
  id4 0.2046 0.1953 0.2760 0.3914
  id4 0.2954 0.3047 0.2240 0.1086