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Nat Methods. 2017 Jun;14(6):590-592. doi: 10.1038/nmeth.4267. Epub 2017 Apr 24.

Genome-wide profiling of heritable and de novo STR variations.

Author information

1
New York Genome Center, New York, New York, USA.
2
Computational and Systems Biology Program, MIT, Cambridge, Massachusetts, USA.
3
Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA.
4
Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
5
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
6
Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.

Abstract

Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool.github.io/HipSTR.

PMID:
28436466
PMCID:
PMC5482724
DOI:
10.1038/nmeth.4267
[Indexed for MEDLINE]
Free PMC Article

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