# Package picard.vcf

package picard.vcf

Related Packages
Package
Description
picard
picard.vcf.filter
picard.vcf.MendelianViolations
picard.vcf.processor
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 nonoverlapping 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.
GenotypeConcordanceStateCodes
Created by kbergin on 7/30/15.
GenotypeConcordanceStates
A class to store the various classifications for: 1.
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.TruthAndCallStates
A minute class to store the truth and call state respectively.
GenotypeConcordanceStates.TruthState
These states represent the relationship between a truth genotype and the reference sequence.
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.
VcfToIntervalList.VARIANT_ID_TYPES
VcfUtils
Created by farjoun on 4/1/17.