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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
A Comprehensive Analysis of the Agreement and Performance of Variant Annotation Programs in Equine Genomes
Jillian L Marlowe1, Lauren Hughes2, Eric Barrey3
1Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, MN 55455, USA.
Genes
|June 26, 2026
Summary
Standardizing terminology is crucial for accurate variant annotation in domestic animals. This study found that consistent terminology significantly improves agreement between tools like Ensembl-VEP, SnpEff, and ANNOVAR, impacting variant prioritization.
Area of Science:
- Genomics
- Bioinformatics
- Animal Genetics
Background:
- Whole-genome sequencing (WGS) is widely used for genetic studies in domestic animals.
- Prioritizing causal variants requires effective variant annotation tools.
- Validation of these tools for non-human genomes is limited.
Purpose of the Study:
- To assess the agreement of popular variant annotators (Ensembl-VEP, SnpEff, ANNOVAR) in domestic animal genomes.
- To identify factors influencing annotation agreement and computational resource usage.
- To provide guidance for selecting variant annotation tools in animal genomics.
Main Methods:
- Evaluated annotation agreement across >58 million variants from 1065 horse genomes.
- Compared Ensembl-VEP, SnpEff, and ANNOVAR performance.
- Assessed impact of terminology standardization and genomic context on agreement.
- Measured computational resource requirements (memory, time).
Main Results:
- High agreement (>90%) achieved when terminology was standardized across annotators.
- Agreement dropped significantly (0-67%) without standardized terminology.
- Exonic and loss-of-function variants showed lower agreement than intergenic variants.
- ANNOVAR had substantially higher memory and time requirements compared to other tools.
Conclusions:
- Tool selection for variant annotation should consider study needs and computational resources.
- Standardization of terminology is critical for reliable variant prioritization in domestic animals.
- Findings offer a resource for optimizing variant annotation strategies in animal genomics research.
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