VCF of insertions and deletions found at high levels in multi breed Equus caballus population

Abstract

Datasets containing high confidence single nucleotide polymorphisms that exist in the genome of horses have previously been published in support of population genetic studies, disease variant discovery, and other type of genetic research. There are no similar datasets for insertions and deletions (indels). Here we created a preliminary set of indels that exist within a certain range of allele frequencies in a large diverse population of apparently healthy horses. A total of ~2M indels passed GATK filtering thresholds and had an allele frequency between 1% and 60%. Though the criteria for inclusion in this dataset are lenient to increase the total numbers these loci are likely to exist in the equine genome and can be used as a preliminary set of indels for some genetic studies. So far this set of indels has been used to create simulated equine genomes that will be used as a benchmarking measure of variant calling and genotyping methods.