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

Detail

  • Operation: Sequencing quality control;Imputation;Repeat sequence analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU GPL v2

  • Cost: Free

  • Version name: -

  • Credit: The Burroughs WellcomeFund, NIJ, Andria and Paul Heafy, the National Human Genome Research Institute of the National Institutes of Health

  • Input: BAM/CRAM, FASTA, str-VCF, BAM-SAMPS, BAM-LIBS

  • Output: viz-out, PDF

  • Contact: hipstrtool@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • Genome-wide profiling of heritable and de novo STR variations.
  • Willems T, et al. Genome-wide profiling of heritable and de novo STR variations. Genome-wide profiling of heritable and de novo STR variations. 2017; 14:590-592. doi: 10.1038/nmeth.4267
  • https://doi.org/10.1038/nmeth.4267
  • PMID: 28436466
  • PMC: PMC5482724

Download and documentation

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