Minor Allele Frequency of Zero Module

The usage of the standalone module is shown below:

$ pyGenClean_flag_maf_zero --help
usage: pyGenClean_flag_maf_zero [-h] [-v] --bfile FILE [--out FILE]

Flags SNPs with MAF of 0.

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: flag_maf_0]

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. Computes the frequencies using Plink.
  2. Finds markers with a MAF of zero.

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. flag_maf_0]):

  1. One file and one set of PLINK’s result file:
    • flag_maf_0.frq: the frequency of each marker in the source dataset.
    • flag_maf_0.list: the list of markers with a minor allele frequency of zero.

The Algorithm

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