InvertypeR

InvertypeR is a software tool designed to improve the discovery, genotyping, and phasing of genomic inversions using single-cell Strand-seq data. It addresses the limitations of conventional methods by utilizing a Bayesian binomial model to genotype inversions based on fixed genomic coordinates. This approach increases the statistical power for detecting more minor inversions (< 10 Kb) and reduces the need for manual inspection to distinguish between true and false positives.

The effectiveness of InvertypeR was validated by re-genotyping inversions reported for three trios by the Human Genome Structural Variation Consortium. The tool significantly reduced the Mendelian discordance in family inversion genotypes from 6.3% to 0.5%. Additionally, by applying InvertypeR to published inversion coordinates, predicted inversion hotspots, and coordinates from conventional inversion discovery, the tool identified 66 previously unreported inversions for the three trios.