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.