BOL

HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by:

1. Learning locus-specific PCR stutter models using an EM algorithm
2. Mining candidate STR alleles from population-scale sequencing data
3. Employing a specialized hidden Markov model to align reads to candidate alleles while accounting for STR artifacts
4. Utilizing phased SNP haplotypes to genotype and phase STRs