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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. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Kristmundsdottir S

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

REPOSITORIES: biostudies-literature

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popSTR2 enables clinical and population-scale genotyping of microsatellites.

Kristmundsdottir Snædis S Eggertsson Hannes P HP Arnadottir Gudny A GA Halldorsson Bjarni V BV

Bioinformatics (Oxford, England) 20200401 7

<h4>Summary</h4>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 g ...[more]

PMID: 31804671

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