| Package | Description |
|---|---|
| picard.vcf |
| Class and Description |
|---|
| CallingMetricAccumulator
Collects variants and generates metrics about them.
|
| CallingMetricAccumulator.Result |
| 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).
|
| 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.
|
| 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.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.
|
| PairedVariantSubContextIterator.VcfTuple
Little class to hold a pair of VariantContexts that are in sync with one another.
|