.. _alt_allele_prob_file_format:

Alternative allele probability file
===================================

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

The ``.alt_allele_prob.txt`` file contains *alternative allele probabilities*
for each base population (metafounder) and each locus.
There is one line per locus, with one optional top/header line.
The header contains the metafounder ID(s),
which can be skipped when there is just one metafounder / no metafounders.
The remaining lines contain the metafounder-specific alternative allele probabilities for each locus.
The file should include all metafounders present in pedigrees.
Any missing values, or whole metafounder columns, default to 0.5 for all loci.
If you do not have information for some loci, provide 0.5 for those loci.
The file format is identical whether inputted via ``-alt_allele_prob_file`` or
outputted from estimation using ``-est_start_alt_allele_prob`` or ``-est_alt_allele_prob``.

Example with no metafounder and four loci:

::

  0.468005
  0.195520
  0.733061
  0.145847


Example with two metafounders and four loci:

::

  MF_1      MF_2
  0.468005  0.390000
  0.195520  0.219890
  0.733061  0.509849
  0.145847  0.090000