ArticleBioinformatics (Oxford, England)2020
popSTR2 enables clinical and population-scale genotyping of microsatellites.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genome-wide detection of somatic mosaicism at short tandem repeats.Bioinformatics (Oxford, England) · 2024Article
- The correlation between CpG methylation and gene expression is driven by sequence variants.Nature genetics · 2024Article
- LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads.Genome biology · 2024Article
- Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data.Molecular ecology resources · 2024Article
- Genome-wide profiling of genetic variation at tandem repeat from long reads.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide detection of somatic mosaicism at short tandem repeats.bioRxiv : the preprint server for biology · 2023Article
- Characterization of genome-wide STR variation in 6487 human genomes.Nature communications · 2023Article
- TRTools: a toolkit for genome-wide analysis of tandem repeats.Bioinformatics (Oxford, England) · 2021Article
- Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.BMC bioinformatics · 2021Article
- Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.Genome biology · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summarypopSTR2 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.
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