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.
Cite
@article{arxiv.1306.2243,
title = {mendelFix: a Perl script for checking Mendelian errors in high density SNP data of trio designs},
author = {Yuri Tani Utsunomiya and Rodrigo Vitorio Alonso and Adriana Santana do Carmo and Francine Campagnari and José Antonio Vinsintin and José Fernando Garcia},
journal= {arXiv preprint arXiv:1306.2243},
year = {2013}
}