vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework.

ABSTRACT

Motivation Genotyping error can impact downstream single nucleotide polymorphism (SNP)-based analyses. Simulating various modes and levels of error can help investigators better understand potential biases caused by miscalled genotypes. Methods: We have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missingness in variant call format (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 the kind and type of error. Software availability: vcferr 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).