popSTR2 enables clinical and population-scale genotyping of microsatellites

Abstract

Summary: popSTR2 is an update and augmentation of our previous work ‘popSTR: a population-based microsatellite genotyper’. To make genotyping sensitive to inter-sample differences, we supply a kernel to estimate sample-specific slippage rates. For clinical sequencing purposes, a panel of known pathogenic repeat expansions is provided along with a script that scans and flags for manual inspection markers indicative of a pathogenic expansion. Like its predecessor, popSTR2 allows for joint genotyping of samples at a population scale. We now provide a binning method that makes the microsatellite genotypes more amenable to analysis within standard association pipelines and can increase association power. Availability and implementation: https://github.com/DecodeGenetics/popSTR. Contact: snaedisk@decode.is or bjarni.halldorsson@decode.is Supplementary information: Supplementary data are available at Bioinformatics online.