Package picard.vcf
Class GenotypeConcordanceStates
java.lang.Object
picard.vcf.GenotypeConcordanceStates
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 ClassesModifier and TypeClassDescriptionstatic enum
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.static enum
A specific state for a 2x2 contingency table.static class
A minute class to store the truth and call state respectively.static enum
These states represent the relationship between a truth genotype and the reference sequence. -
Constructor Summary
Constructors -
Method Summary
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Constructor Details
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GenotypeConcordanceStates
public GenotypeConcordanceStates()
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