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.

SUBMITTER: Kristmundsdottir S 

PROVIDER: S-EPMC7141861 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature