vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

Abstract

MotivationGenotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes. ResultsWe have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in VCF files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of kind and type of error. Software Availabilityvcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).