| Class | Description |
|---|---|
| AGPMap | |
| BackwardForwardAlgorithm | |
| BackwardForwardVariableStateNumber | |
| BiparentalHaplotypeFinder | |
| CallParentAllelesPlugin | |
| ClusterGenotypesPlugin | |
| CrossProgenyEmissionMatrix | |
| EmissionProbability | |
| FILLINDonorGenotypeUtils |
Methods for loading the donor haplotype files and for arranging the bit states (Major versus Minor) if they differ between the donor genotypes and the target genotypes
|
| FILLINFindHaplotypesPlugin |
Creates haplotypes by finding large IBS regions within GBS data. Starts with the highest coverage taxa and looks within windows of near perfect matches. Combines all matches together into one haplotype. The haplotype is named for the highest coverage sample.
|
| FILLINImputationAccuracy |
A class to mask input files, hold information related to accuracy calculation, and calculate accuracy for FILLINImputationPlugin
|
| FILLINImputationPlugin |
FILLIN imputation relies on a libary of haplotypes and uses nearest neighbor searches followed by HMM Viterbi resolution or block-based resolution. It is the best approach for substantially unrelated taxa in TASSEL. BEAGLE4 is a better approach currently for landraces, while FILLIN outperforms if there is a good reference set of haplotypes.
|
| FILLINImputationUtils |
Basic utility functions to support imputation by blocks.
|
| FSFHapImputationPlugin | |
| FindMergeHaplotypesPlugin |
Creates haplotypes by finding large IBS regions within GBS data. Starts with the highest coverage taxa and looks within windows of near perfect matches. Combines all matches together into one haplotype. The haplotype is named for the highest coverage sample. TODO: 1. plus add short inbred segments not present full ones 2. Cluster and choose haplotypes by cluster and number of new minor alleles (or information) 3. Set max het frequency as a setting
|
| ImputationAccuracyPlugin |
This evaluates the accuracy of an imputed genotype. First input genotype should be the original. Second should be the masked genotype. Third should be the imputed genotype.
|
| ImputationUtils | |
| ImputeCrossProgeny | |
| ImputeProgenyStatesPlugin | |
| LDKNNiImputationHetV2Plugin |
This imputation algorithm uses LD to identify good predictors for each SNP, and then uses the high LD SNPs to identify K- Nearest Neighbors. The genotype is called with a weighted mode of the KNNs.
|
| LDKNNiImputationHetV3Plugin |
This imputation algorithm uses LD to identify good predictors for each SNP, and then uses the high LD SNPs to identify K- Nearest Neighbors. The genotype is called with a weighted mode of the KNNs.
|
| LDKNNiImputationPlugin |
This imputation algorithm uses LD to identify good predictors for each SNP, and then uses the high LD SNPs to identify K- Nearest Neighbors. The genotype is called with a weighted mode of the KNNs.
|
| MergeBreakpointFilesPlugin | |
| NucleotideImputationUtils | |
| ParentPhasingPlugin | |
| PhaseHighCoverage | |
| PopulationData | |
| RandomGenotypeImputationPlugin | |
| ReImputeUpdatedTaxaByFILLINPlugin |
Compares an unfinished HDF5 file containing raw genotypes to a corresponding unfinished HDF5 file containing FILLIN-imputed genotypes to find new taxa (or taxa with additional depth) in the raw geno file, then imputes (or reimputes) these with FILLIN and adds them to (or replaces them in) the imputed geno file. This is part of the Automated Production Pipeline.
|
| RemoveIndelsForBeaglePlugin | |
| RephaseParents | |
| SelfedHaplotypeFinder | |
| SubpopulationFinder | |
| TransitionProbability | |
| TransitionProbabilityWithVariableRecombination | |
| UseParentHaplotypes | |
| ViterbiAlgorithm | |
| ViterbiAlgorithmPlugin | |
| ViterbiAlgorithmVariableStateNumber | |
| WritePopulationAlignmentPlugin |