popSTR2 enables clinical and population-scale genotyping of microsatellites

• DOI: 10.1093/bioinformatics/btz913
• Publication Date: 2019-12-03T12:14:01Z
• Authors: Snædis Kristmunds...; Hannes P Eggertsson; Gudny A Arnadottir; Bjarni V Halldorsson
• Keywords: Genotype; 0206 medical engineering; 02 engineering and technology; Applications Notes; Software; Microsatellite Repeats; 3. Good health

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.

Supplementary information Supplementary data are available at Bioinformatics online.