| Class | Description |
|---|---|
| ByIntervalListVariantContextIterator |
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
|
| CallingMetricAccumulator |
Collects variants and generates metrics about them.
|
| CallingMetricAccumulator.Result | |
| CollectVariantCallingMetrics |
Collects summary and per-sample metrics about variant calls in a VCF file.
|
| CollectVariantCallingMetrics.VariantCallingDetailMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
|
| CollectVariantCallingMetrics.VariantCallingSummaryMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
|
| GA4GHScheme |
The scheme is defined in the constructor.
|
| GA4GHSchemeWithMissingAsHomRef |
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
|
| GatherVcfs |
Simple little class that combines multiple VCFs that have exactly the same set of samples
and totally discrete sets of loci.
|
| GenotypeConcordance |
Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference)
the other being the call.
|
| GenotypeConcordanceContingencyMetrics |
Class that holds metrics about the Genotype Concordance contingency tables.
|
| GenotypeConcordanceCounts |
A class to store the counts for various truth and call state classifications relative to a reference.
|
| GenotypeConcordanceDetailMetrics |
Class that holds detail metrics about Genotype Concordance
|
| GenotypeConcordanceScheme |
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
|
| GenotypeConcordanceSchemeFactory |
Created by kbergin on 6/19/15.
|
| GenotypeConcordanceStates |
A class to store the various classifications for:
1.
|
| GenotypeConcordanceStates.TruthAndCallStates |
A minute class to store the truth and call state respectively.
|
| GenotypeConcordanceSummaryMetrics |
Class that holds summary metrics about Genotype Concordance
|
| GvcfMetricAccumulator |
An accumulator for collecting metrics about a single-sample GVCF.
|
| LiftoverVcf |
Tool for lifting over a VCF to another genome build and producing a properly header'd,
sorted and indexed VCF in one go.
|
| MakeSitesOnlyVcf |
Writes out a VCF that contains all the site-level information for all records in the input VCF and no per-sample information.
|
| MergeVcfs |
Combines multiple VCF files into a single file.
|
| PairedVariantSubContextIterator |
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
|
| PairedVariantSubContextIterator.VcfTuple |
Little class to hold a pair of VariantContexts that are in sync with one another.
|
| RenameSampleInVcf | |
| SortVcf |
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then
by coordinate.
|
| SplitVcfs |
Splits the input VCF file into two, one for indels and one for SNPs.
|
| UpdateVcfSequenceDictionary |
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
|
| VcfFormatConverter |
Converts an ASCII VCF file to a binary BCF or vice versa.
|
| VcfToIntervalList |
Creates an interval list from a VCF
|
| Enum | Description |
|---|---|
| GenotypeConcordanceStateCodes |
Created by kbergin on 7/30/15.
|
| GenotypeConcordanceStates.CallState |
These states represent the relationship between the call genotype and the truth genotype relative to
a reference sequence.
|
| GenotypeConcordanceStates.ContingencyState |
A specific state for a 2x2 contingency table.
|
| GenotypeConcordanceStates.TruthState |
These states represent the relationship between a truth genotype and the reference sequence.
|