Package phase

Class PbwtPhaser

java.lang.Object
phase.PbwtPhaser
public class PbwtPhaser extends Object

Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)

Instances of class PbwtPhaser are not thread-safe.

Reference: Richard Durbin. (2014) Efficient haplotype matching and storage using the Positional Burrows-Wheeler Transform (PBWT). Bioinformatics 30(9):1266-72.

Reference: Olivier Delaneau, Jean-Francois Zagury, Matthew R Robinson, Jonathan Marchini, Emmanouil Dermitzakis. (2019) Accurate, scalable and integrative haplotype estimation. Nature Communications 10(1):5436.

  • Method Details

    • initPhase

      public static AtomicReferenceArray<SamplePhase> initPhase(FixedPhaseData fpd, long seed)
      Returns an initial phasing for first-stage markers in the target samples.
      Parameters:
      fpd - the input data for phasing
      seed - seed for random number generation
      Returns:
      an initial genotype phasing for the first-stage markers in the target samples
      Throws:
      NullPointerException - if fpd == null