Marker Missingness Module

The usage of the standalone module is shown below:

$ pyGenClean_snp_missingness --help
usage: pyGenClean_snp_missingness [-h] [-v] --bfile FILE [--geno FLOAT]
                                  [--out FILE]

Computes marker missingness using Plink.

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,

  --geno FLOAT   The missingness threshold (remove SNPs with more than x
                 percent missing genotypes). [Default: 0.020]

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

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. Runs Plink to remove markers with a missing rate above a user defined threshold.
  2. Finds the markers that were removed (those that have a missing rate above the user defined threshold.

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. clean_geno]):

  1. One set of Plink output files:
    • clean_geno.fam: the dataset with markers having a high missing rate removed (according to a user defined threshold).
  2. One custom file:
    • clean_geno.removed_snps: a list of markers that have a high missing rate (above a user defined threshold).

The Algorithm

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