Genomic variant benchmark: if you cannot measure it, you cannot improve it

doi:10.1186/s13059-023-03061-1

Genomic variant benchmark: if you cannot measure it, you cannot improve it

2023-10-05

8

OA

AI

S

Sina Majidian

D

Daniel Paiva Agustinho

DOI：10.1186/s13059-023-03061-1

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Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.

Keywords:

Genetic variation

SNPs

Indels

Structural variant

Benchmark datasets

Medical genes

Sequencing technology

Genomic variant benchmark: if you cannot measure it, you cannot improve it

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