Genome-wide profiling of heritable and de novo STR variations

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


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

MeSH terms

  • Algorithms
  • Chromosome Mapping / methods*
  • DNA Fingerprinting / methods*
  • Genetic Predisposition to Disease / genetics*
  • Genetic Variation / genetics*
  • Genome, Human / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Microsatellite Repeats / genetics*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software