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.
Sequence composition, complexity and repeats; Genomics; Sequencing
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
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