Package picard.vcf

Class Summary

Class	Description
AccumulateVariantCallingMetrics	Combines multiple Variant Calling Metrics files into a single file.
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).
FixVcfHeader	Tool for replacing or fixing up a VCF header.
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	Summary
GenotypeConcordance.Alleles	A simple structure to return the results of getAlleles.
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	Summary
MakeSitesOnlyVcf	Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeVcfSampleNameMap	Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MergeVcfs	Combines multiple variant files into a single variant 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	Renames a sample within a VCF or BCF.
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	Converts a VCF or BCF file to a Picard Interval List.
VcfUtils	Created by farjoun on 4/1/17.

Enum Summary

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.