Interface | Description |
---|---|
StateProbs |
Class
StateProbs stores a subset of Li and Stephens HMM states
and associated probabilities for a target haplotype. |
Class | Description |
---|---|
HaplotypeCoder |
Class
HaplotypeCoder indexes the observed allele sequences
in phased reference and target genotype data in a chromosome interval. |
ImpData |
Class
ImpData contains the input data for imputation of
ungenotyped markers. |
ImpIbs |
Class
ImpIbs identifies haplotypes that share a long
IBS segment with a specified haplotype. |
ImpLS |
Class
ImpLS computes HMM state probabilities
at genotyped markers in the target haplotypes. |
ImpLSBaum |
Class
ImpLSBaum implements a Baum hidden Markov model
forward and backward algorithms for computing HMM state probabilities
at genotyped markers using IBS-matched reference haplotypes. |
ImpStates |
Class
ImpStates identifies a list of pseudo-reference haplotypes
for a target haplotype. |
ImputedRecBuilder |
Class
ImputeRecBuilder contains methods for constructing
and printing a VCF record in VCF 4.3 format. |
ImputedVcfWriter |
Class
ImputedVcfWriter writes observed and imputed genotypes
to a VCF output file. |
RefHapHash |
Class
RefHapHash stores a hash code for each haplotype
in a sublist of reference haplotypes. |
StateProbsFactory |
Class
StateProbsFactory stores HMM state probabilities
that that can be used to imputed impute missing HMM state probabilities
using linear interpolation. |