picard.vcf

Class GenotypeConcordanceDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.vcf.GenotypeConcordanceDetailMetrics

public class GenotypeConcordanceDetailMetrics
extends htsjdk.samtools.metrics.MetricBase

Class that holds detail metrics about Genotype Concordance

Author:

George Grant

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	CALL_SAMPLE The name of the 'call' sample
GenotypeConcordanceStates.CallState	CALL_STATE The state of the 'call' sample (i.e.
java.lang.String	CONTINGENCY_VALUES The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
long	COUNT The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
java.lang.String	TRUTH_SAMPLE The name of the 'truth' sample
GenotypeConcordanceStates.TruthState	TRUTH_STATE The state of the 'truth' sample (i.e.
htsjdk.variant.variantcontext.VariantContext.Type	VARIANT_TYPE The type of the event (i.e.

Constructor Summary

Constructors

Constructor and Description
GenotypeConcordanceDetailMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

VARIANT_TYPE

public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE

The type of the event (i.e. either SNP or INDEL)

TRUTH_SAMPLE

public java.lang.String TRUTH_SAMPLE

The name of the 'truth' sample

CALL_SAMPLE

public java.lang.String CALL_SAMPLE

The name of the 'call' sample

TRUTH_STATE

public GenotypeConcordanceStates.TruthState TRUTH_STATE

The state of the 'truth' sample (i.e. HOM_REF, HET_REF_VAR1, HET_VAR1_VAR2...)

CALL_STATE

public GenotypeConcordanceStates.CallState CALL_STATE

The state of the 'call' sample (i.e. HOM_REF, HET_REF_VAR1...)

COUNT

public long COUNT

The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs

CONTINGENCY_VALUES

public java.lang.String CONTINGENCY_VALUES

The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference. In general, we are comparing two sets of alleles. Therefore, we can have zero or more contingency table values represented in one comparison. For example, if the truthset is a heterozygous call with both alleles non-reference (HET_VAR1_VAR2), and the callset is a heterozygous call with both alleles non-reference with one of the alternate alleles matching an alternate allele in the callset, we would have a true positive, false positive, and false negative. The true positive is from the matching alternate alleles, the false positive is the alternate allele found in the callset but not found in the truthset, and the false negative is the alternate in the truthset not found in the callset. We also include a true negative in cases where the reference allele is found in both the truthset and callset.

Constructor Detail

GenotypeConcordanceDetailMetrics

public GenotypeConcordanceDetailMetrics()