picard.vcf

Class CollectVariantCallingMetrics.VariantCallingDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics

picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics

Enclosing class:

CollectVariantCallingMetrics

public static class CollectVariantCallingMetrics.VariantCallingDetailMetrics
extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics

A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.

Field Summary

Fields

Modifier and Type	Field and Description
double	HET_HOMVAR_RATIO (count of hets)/(count of homozygous non-ref) for this sample
java.lang.String	SAMPLE_ALIAS The name of the sample being assayed

Fields inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics

DBSNP_INS_DEL_RATIO, DBSNP_TITV, FILTERED_INDELS, FILTERED_SNPS, NOVEL_INDELS, NOVEL_INS_DEL_RATIO, NOVEL_SNPS, NOVEL_TITV, NUM_IN_DB_SNP, NUM_IN_DB_SNP_COMPLEX_INDELS, NUM_IN_DB_SNP_INDELS, NUM_IN_DB_SNP_MULTIALLELIC, NUM_SINGLETONS, PCT_DBSNP, PCT_DBSNP_INDELS, SNP_REFERENCE_BIAS, TOTAL_COMPLEX_INDELS, TOTAL_INDELS, TOTAL_MULTIALLELIC_SNPS, TOTAL_SNPS

Constructor Summary

Constructors

Constructor and Description
VariantCallingDetailMetrics()

Method Summary

Modifier and Type	Method and Description
static void	foldInto(CollectVariantCallingMetrics.VariantCallingDetailMetrics target, java.util.Collection<CollectVariantCallingMetrics.VariantCallingDetailMetrics> metrics)
static java.lang.String	getFileExtension()
void	updateDerivedValuesInPlace()

Methods inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics

foldInto

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

SAMPLE_ALIAS

public java.lang.String SAMPLE_ALIAS

The name of the sample being assayed

HET_HOMVAR_RATIO

public double HET_HOMVAR_RATIO

(count of hets)/(count of homozygous non-ref) for this sample

Constructor Detail

VariantCallingDetailMetrics

public VariantCallingDetailMetrics()

Method Detail

getFileExtension

public static java.lang.String getFileExtension()

foldInto

public static void foldInto(CollectVariantCallingMetrics.VariantCallingDetailMetrics target,
                            java.util.Collection<CollectVariantCallingMetrics.VariantCallingDetailMetrics> metrics)

updateDerivedValuesInPlace

public void updateDerivedValuesInPlace()

Overrides:

updateDerivedValuesInPlace in class CollectVariantCallingMetrics.VariantCallingSummaryMetrics