Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq.

Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.