VarCover: Allele Min-Set Cover Software

To facilitate reference material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and pre-selection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of 1000 Genomes (1KG) Project reference samples to cover 237 putatively pathogenic variants (of which 12 were pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG).

Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Erick R. Scott, Vikas Bansal, Carl Meacham, Stuart A. Scott Tags: Technical Advance Source Type: research