Broad Insitute

Variant calling from whole-genome sequencing data plays a crucial role in medical genetics, population genetics, and clinical genetic testing. Many algorithms have been developed for accurate variant calling from short-read data [1–4], and multiple benchmarks have been conducted to evaluate their accuracy [5, 6]. A common practice in variant calling evaluation is to compare called variants to curated ground truth, notably generated by the Genome-In-A-Bottle (GIAB) group [5].

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The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome. We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes.