mendelFix: a Perl script for checking Mendelian errors in high density SNP data of trio designs

TL;DR

mendelFix is a Perl tool designed to identify and correct Mendelian errors in high-density SNP data from trio family designs, facilitating quality control and genotype inference in genetic studies.

Contribution

It introduces a simple, integrated software solution for error checking and genotype inference in trio-based SNP datasets, streamlining data quality control.

Findings

Effective detection of Mendelian errors in SNP data

Automatic correction of inconsistent genotypes

Genotype inference based on parental information

Abstract

Here we present mendelFix, a Perl script for checking Mendelian errors in genome-wide SNP data of trio designs. The program takes 12-recoded PLINK PED and MAP files as input to calculate a series of summary statistics for Mendelian errors, sets missing offspring genotypes that present Mendelian inconsistencies, and implements a simplistic procedure to infer missing genotypes using parent information. The program can be easily incorporated in any pipeline for family-based SNP data analysis, and is distributed as free software under the GNU General Public License.