Package picard.vcf
Class GenotypeConcordanceDetailMetrics
- java.lang.Object
-
- htsjdk.samtools.metrics.MetricBase
-
- picard.vcf.GenotypeConcordanceDetailMetrics
-
@DocumentedFeature(groupName="Metrics", summary="Metrics") public class GenotypeConcordanceDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Class that holds detail metrics about Genotype Concordance
-
-
Field Summary
Fields Modifier and Type Field Description String
CALL_SAMPLE
The name of the 'call' sampleGenotypeConcordanceStates.CallState
CALL_STATE
The state of the 'call' sample (i.e.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 SAMPLEsString
TRUTH_SAMPLE
The name of the 'truth' sampleGenotypeConcordanceStates.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 Description GenotypeConcordanceDetailMetrics()
-
-
-
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 String TRUTH_SAMPLE
The name of the 'truth' sample
-
CALL_SAMPLE
public 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 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.
-
-