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Review
. 2022 Aug;43(8):976-985.
doi: 10.1002/humu.24311. Epub 2021 Dec 16.

Variant calling: Considerations, practices, and developments

Stepanka Zverinova  1 , Victor Guryev  1
Affiliations
Review

Variant calling: Considerations, practices, and developments

Stepanka Zverinova et al. Hum Mutat. 2022 Aug.

Abstract

The success of many clinical, association, or population genetics studies critically relies on properly performed variant calling step. The variety of modern genomics protocols, techniques, and platforms makes our choices of methods and algorithms difficult and there is no "one size fits all" solution for study design and data analysis. In this review, we discuss considerations that need to be taken into account while designing the study and preparing for the experiments. We outline the variety of variant types that can be detected using sequencing approaches and highlight some specific requirements and basic principles of their detection. Finally, we cover interesting developments that enable variant calling for a broad range of applications in the genomics field. We conclude by discussing technological and algorithmic advances that have the potential to change the ways of calling DNA variants in the nearest future.

Keywords: best practices; genome sequencing; method development; variant calling.

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Figures

Figure 1
Figure 1
Overview of experimental factors that are important for planning and performing a genome sequencing study
Figure 2
Figure 2
Diversity of DNA variant types. (a) Variants that can be discovered by comparing reference genomes and mapped NGS reads. (b) Identification of structural variants using signatures from mapped read pairs. MEI, mobile element insertions; MNV, multi‐nucleotide variants; NRS, non‐reference sequences; SNV, single nucleotide variants; SV, structural variants
Figure 3
Figure 3
Current developments and challenges in variant identification technologies and algorithms
See this image and copyright information in PMC

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