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

Nagraj, V. P.; Scholz, M.; Jessa, S.; Ge, J.; Woerner, A. E.; Huang, M.; Budowle, B.; Turner, S. D.

2022-06-07 bioinformatics
10.1101/2022.03.28.485853 bioRxiv
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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).

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