Heterozygous Haploid Module

The usage of the standalone module is shown below:

$ pyGenClean_remove_heterozygous_haploid --help
Usage: pyGenClean_remove_heterozygous_haploid [-h] [-v] --bfile FILE
                                              [--out FILE]

Removes heterozygous haploid genotypes.

Optional arguments:
  -h, --help     show this help message and exit
  -v, --version  show program's version number and exit

Input File:
  --bfile FILE   The input file prefix (will find the plink binary files by
                 appending the prefix to the .bim, .bed and .fam files,

Output File:
  --out FILE     The prefix of the output files. [default:

Input Files

This module uses PLINK’s binary file format (bed, bim and fam files) for the source data set (the data of interest).


Here are the steps performed by the module:

  1. Uses Plink to remove the heterozygous haploid genotypes.

Output Files

The output files of each of the steps described above are as follow (note that the output prefix shown is the one by default [i.e. without_hh_genotypes]):

  1. On set of Plink’s output files:
    • without_hh_genotypes: the data set with heterozygous haploid genotypes removed.

The Algorithm

For more information about the actual algorithms and source codes, refer to the following page.