For better experience, turn on JavaScript!


hipSTR

hipSTR

HipSTR (Haplotype inference and phasing for Short Tandem Repeats) is a tool to genotype, phase short tandem repeats (STRs), and to analyze and validate de novo STR mutations genome-wide. HipSTR also includes a function to visualize the supporting reads. The HipSTR algorithm uses an EM algorithm to learn locus-specific PCR stutter models, a hidden Markov model (HMM) to align reads to candidate alleles avoiding STR artifacts, and phased SNP haplotypes for genotyping and phasing.

Topic

Sequence composition, complexity and repeats; Genomics; Sequencing

Details

  • Operation: Sequencing quality control; Imputation; Repeat sequence analysis
  • Input: BAM/CRAM, FASTA, str-VCF, BAM-SAMPS, BAM-LIBS
  • Output: viz-out, PDF
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: The Burroughs WellcomeFund, NIJ, Andria and Paul Heafy, the National Human Genome Research Institute of the National Institutes of Health
  • Contact: hipstrtool _at_ gmail.com
  • Collection: -

Publications

Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y "Genome-wide profiling of heritable and de novo STR variations." Nat. Methods 2017; 14(6):590-592 https://doi.org/10.1038/nmeth.4267
PMID: 28436466
PMCID: PMC5482724


Download and documentation




You may also like:



If you find errors, please report here.