| AccumulateVariantCallingMetrics |
Combines multiple Variant Calling Metrics files into a single file.
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| ByIntervalListVariantContextIterator |
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
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| CallingMetricAccumulator |
Collects variants and generates metrics about them.
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| CallingMetricAccumulator.Result |
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| CollectVariantCallingMetrics |
Collects summary and per-sample metrics about variant calls in a VCF file.
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| CollectVariantCallingMetrics.VariantCallingDetailMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
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| CollectVariantCallingMetrics.VariantCallingSummaryMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
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| FixVcfHeader |
Tool for replacing or fixing up a VCF header.
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| GA4GHScheme |
The scheme is defined in the constructor.
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| GA4GHSchemeWithMissingAsHomRef |
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
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| GatherVcfs |
Simple little class that combines multiple VCFs that have exactly the same set of samples
and nonoverlapping sets of loci.
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| GenotypeConcordance |
Summary
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| GenotypeConcordance.Alleles |
A simple structure to return the results of getAlleles.
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| GenotypeConcordanceContingencyMetrics |
Class that holds metrics about the Genotype Concordance contingency tables.
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| GenotypeConcordanceCounts |
A class to store the counts for various truth and call state classifications relative to a reference.
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| GenotypeConcordanceDetailMetrics |
Class that holds detail metrics about Genotype Concordance
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| GenotypeConcordanceScheme |
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
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| GenotypeConcordanceSchemeFactory |
Created by kbergin on 6/19/15.
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| GenotypeConcordanceStates |
A class to store the various classifications for:
1.
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| GenotypeConcordanceStates.TruthAndCallStates |
A minute class to store the truth and call state respectively.
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| GenotypeConcordanceSummaryMetrics |
Class that holds summary metrics about Genotype Concordance
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| GvcfMetricAccumulator |
An accumulator for collecting metrics about a single-sample GVCF.
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| LiftoverVcf |
Summary
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| MakeSitesOnlyVcf |
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
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| MakeVcfSampleNameMap |
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
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| MergeVcfs |
Combines multiple variant files into a single variant file.
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| PairedVariantSubContextIterator |
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
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| PairedVariantSubContextIterator.VcfTuple |
Little class to hold a pair of VariantContexts that are in sync with one another.
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| RenameSampleInVcf |
Renames a sample within a VCF or BCF.
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| SortVcf |
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then
by coordinate.
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| SplitVcfs |
Splits the input VCF file into two, one for indels and one for SNPs.
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| UpdateVcfSequenceDictionary |
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
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| VcfFormatConverter |
Converts an ASCII VCF file to a binary BCF or vice versa.
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| VcfToIntervalList |
Converts a VCF or BCF file to a Picard Interval List.
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| VcfUtils |
Created by farjoun on 4/1/17.
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