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

2013/06/10 by Utsunomiya, Yuri Tani, Alonso, Rodrigo Vitorio, Carmo, Adriana Santana do +3
#FOS: Biological sciences #Genomics (q-bio.GN)

paper · doi:10.48550/arxiv.1306.2243

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.

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