A workflow to generate a variant catalogue from whole genome sequences

Variant catalogues are essential tools for the diagnosis of patients with rare genetic diseases. However, patients from systematically and structurally excluded populations are lacking representation in variant catalogues such as gnomAD, reducing their diagnosis chances. To address this inequity, population specific variant catalogues are developed, such as the Indigenous Background Variant Library (IBVL) as part of the Silent Genomes Project in Canada. To generate the IBVL, we developed a pipeline calling SNV and mitochondrial variants for GRCh37 and GRCh38 reference genomes. Future updates will include Structural Variants, Mobile Element Insertions, and Short Tandem Repeats. The pipeline can run on local servers to maintain Indigenous data sovereignty, and is modular to allow each project to use as much or as little of the pipeline as they wish. We hope that, by making this pipeline available, more populations around the world will have good and extensive variant catalogues.