EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization
Keywords: 
Single-nucleotide variant
EMVC-2
Issue Date: 
2024
Publisher: 
Oxford University Press
Project: 
info:eu-repo/grantAgreement/AEI/Proyectos de I+D+I (Generación de Conocimiento y Retos Investigación)/PID2021-126718OA-I00/[ES]/NUEVA APROXIMACION COMPUTACIONAL PARA LA CARACTERIZACION DE LOS MECANISMOS DE REGULACION DE CELULAS CANCERIGENAS DESDE DATOS DE SINGLE-CELL
ISSN: 
1367-4811
Note: 
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Citation: 
Dufort-y-Álvarez, G. (Guillermo); Xargay-Ferrer, M. (Martí); Pages-Zamora, A. (A.); et al. "EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization". Bioinformatics. 40 (3), 2024, btad681
Abstract
Motivation Single-nucleotide variants (SNVs) are the most common type of genetic variation in the human genome. Accurate and efficient detection of SNVs from next-generation sequencing (NGS) data is essential for various applications in genomics and personalized medicine. However, SNV calling methods usually suffer from high computational complexity and limited accuracy. In this context, there is a need for new methods that overcome these limitations and provide fast reliable results. Results We present EMVC-2, a novel method for SNV calling from NGS data. EMVC-2 uses a multi-class ensemble classification approach based on the expectation–maximization algorithm that infers at each locus the most likely genotype from multiple labels provided by different learners. The inferred variants are then validated by a decision tree that filters out unlikely ones. We evaluate EMVC-2 on several publicly available real human NGS data for which the set of SNVs is available, and demonstrate that it outperforms state-of-the-art variant callers in terms of accuracy and speed, on average. Availability and implementation EMVC-2 is coded in C and Python, and is freely available for download at: https://github.com/guilledufort/EMVC-2. EMVC-2 is also available in Bioconda.

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