Package picard.vcf
Class GenotypeConcordanceStates
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- picard.vcf.GenotypeConcordanceStates
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public class GenotypeConcordanceStates extends Object
A class to store the various classifications for: 1. a truth genotype versus a reference 2. a call genotype versus a truth, relative to a reference An example use of this class is to have one instance per following use case: - SNPs - indels - filtered variant (truth or call) - filtered genotype (truth or call) - low GQ (call) - low DP (call) - No call (truth or call) - No variant (truth or call) *
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
GenotypeConcordanceStates.CallState
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.static class
GenotypeConcordanceStates.ContingencyState
A specific state for a 2x2 contingency table.static class
GenotypeConcordanceStates.TruthAndCallStates
A minute class to store the truth and call state respectively.static class
GenotypeConcordanceStates.TruthState
These states represent the relationship between a truth genotype and the reference sequence.
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Constructor Summary
Constructors Constructor Description GenotypeConcordanceStates()
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