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Background  Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed.    Results  We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate.    Conclusions  This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1700-4) contains supplementary material, which is available to authorized users.

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants