# 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,
respectively.

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).

## Procedure¶

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.