pb-StarPhase v0.11.0

Changes

• The underlying methodology has been significantly altered to improve CYP2D6 diplotyping in targeted sequencing
  • The core CYP2D6 regions have been shrunk to contain just the regions containing variants that define the allele
  • Additional regions have been added solely for the purpose of linking CYP2D6 alleles: REP6, REP7, spacer, and "link_region" (region between CYP2D6 and CYP2D7 typically)
  • The chaining algorithm has been altered to account for the additional regions above. A "normal" haplotype chain is expected to have the following order of regions in GRCh38: REP6 -> CYP2D6 -> link_region -> REP7 -> spacer -> CYP2D7
  • The scoring of diplotype chain pairs is now based on a unified scoring scheme that accounts for: 1) edit distance of observations to the chain pair, 2) likelihood of the chain pair based on allele coverage and multinomial, 3) lasso penalty for duplications, and 4) penalty for unexpected chain events (see above "normal" chain)
  • The debug BAM will now output a haplotype block for each identified region (e.g., REP6 will have its own block)