<![CDATA[BOL: HipSTR: Haplotype inference and phasing for Short Tandem Repeats]]> https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats? https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats Thu, 07 Mar 2019 21:13:06 -0600 https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats <![CDATA[HipSTR: Haplotype inference and phasing for Short Tandem Repeats]]> 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

Address of the bookmark: https://github.com/tfwillems/HipSTR

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