| Class | Description |
|---|---|
| AddReferenceAlleleToHDF5Plugin | |
| AddReferenceToGenotypePlugin | |
| AdjustPhasingPlugin | |
| BuildUnfinishedHDF5GenotypesPlugin |
Opens an "unfinished" HDF5 genotypes file, on which .closeUnfinished() was called rather than .build() and finalizes it by calling .build(). If an output file name is provided, then the input file is first copied to that, and then build() is called on that copy. If provided, root level annotations DataSetName and DataSetDescription are also added. "__DATE__" in the provided dataSet name is replaced a current date stamp ("_yyyyMMdd"). "__SNPS__" and "__TAXA__" in the dataSetDescription are replaced with the number of sites and taxa, respectively.
|
| CombineDataSetsPlugin | |
| ConvertAlignmentCoordinatesPlugin | |
| CountAssociationsPlugin | |
| CountAssociationsPluginKt | |
| CreateHybridGenotypesPlugin | |
| ExportMultiplePlugin | |
| ExportPlugin | |
| ExtractHapmapSubsetPlugin | |
| FeatureListToPositionsPlugin | |
| FileLoadPlugin | |
| FindInversionsPlugin | |
| GenomeAnnosDBQueryToPositionListPlugin |
Reads a PostgreSQL query file and a genomeAnnosDB connection config file, checks that the query is a SELECT query for chr, position, etc.., executes the query, and turns the results into a PositionList with any result fields other that chr & position added as annotations.
|
| GenosToABHPlugin |
Plugin to convert genotypes to parental comparisons and store them in an output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or parent B's genotype respectively. If the genotype is neither A or B or a het combination of A/B (B/A) then it is coded as "NA".
|
| GenotypeSummaryPlugin | |
| GenotypeToAdditiveValuesPlugin | |
| GetPositionListPlugin | |
| GetTaxaListPlugin | |
| HDF5SummaryPlugin |
Created by jgw87 on 5/28/14. This plugin is meant to take an HDF5 file and output a report of various summary statistics or information. INclude
|
| HetsToUnknownPlugin | |
| IdentityRecognitionPlugin | |
| IndelsToUnknownPlugin | |
| IntersectionAlignmentPlugin | |
| KmerCountingPlugin | |
| KmerCountingPluginKt | |
| LIXPlugin | |
| LowLevelCopyOfHDF5 |
Provides low level copy and migration tool.
|
| MaskGenotypePlugin |
The purpose of this class is to mask (make UNKNOWN) a portion of the genotypes of the given GenotypeTable. The resulting GenotypeTable will be the same except some genotypes will have been changed to Unknown.
|
| MeanR2FromLDPlugin | |
| MemoryUsagePlugin | |
| MergeAlignmentsSameSitesPlugin | |
| MergeGenotypeTablesPlugin |
Merge alignments into a single alignment containing all taxa and positions. TODO: Add capacity for depth
|
| MergeGenotypeTablesPluginV2 | |
| MergeHDF5GenotypesSameSitesPlugin | |
| MergeRenameDeleteTaxaPlugin | |
| MigrateHDF5FromT4T5 |
Provides a migration tool from TASSEL4 HDF5 to TASSEL5 HDF5
|
| PassThroughPlugin | |
| PlinkLoadPlugin | |
| PrincipalComponentsPlugin | |
| ProjectPcsAndRunModelSelectionPlugin | |
| ProjectionLoadPlugin | |
| SeparatePlugin | |
| SetLowDepthGenosToMissingPlugin |
Set genotypes below a minimum depth to missing. Set each genotype in the input genotypes to missing if the underlying allelic depth is below a user- specified minimum. Input: GenotypeTable stored as a Datum within a DataSet Output: GenotypeTable stored as a Datum within a DataSet
|
| SortGenotypeFilePlugin |
Created by jgw87 on 6/5/14. This plugin takes a Hapmap or VCF genotype file and sorts it according to TASSEL's conventions which rely on the position, locus (chromosome), strand, and SNP name (to facilitate searching).
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| SortTaxaAlphabeticallyPlugin | |
| SplitHDF5ByChromosomePlugin | |
| SubtractGenotypesPlugin | |
| SynonymizerPlugin | |
| ThinSitesByPositionPlugin |
Plugin to thin out sites based on their physical position on the chromosome. Expects the user to enter a minimum distance between sites in base pair. Accepts and writes .hmp.txt, .hmp.txt.gz, .vcf, .vcf.gz and .h5 files.
|
| UnionAlignmentPlugin |