Package picard.vcf
Class CollectVariantCallingMetrics.VariantCallingDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
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- picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
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- Enclosing class:
- CollectVariantCallingMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") 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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
Fields Modifier and Type Field Description double
HET_HOMVAR_RATIO
(count of hets)/(count of homozygous non-ref) for this sampledouble
PCT_GQ0_VARIANTS
The percentage of variants in a particular sample that have a GQ score of 0.String
SAMPLE_ALIAS
The name of the sample being assayedlong
TOTAL_GQ0_VARIANTS
The total number of variants in a particular sample that have a GQ score of 0.long
TOTAL_HET_DEPTH
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample-
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
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Constructor Summary
Constructors Constructor Description VariantCallingDetailMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calculateDerivedFields()
Placeholder method that will calculate the derived fields from the other ones.void
calculateFromDerivedFields()
static String
getFileExtension()
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Methods inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateFromDerivedFields, foldInto
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed
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HET_HOMVAR_RATIO
public double HET_HOMVAR_RATIO
(count of hets)/(count of homozygous non-ref) for this sample
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PCT_GQ0_VARIANTS
public double PCT_GQ0_VARIANTS
The percentage of variants in a particular sample that have a GQ score of 0.
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TOTAL_GQ0_VARIANTS
public long TOTAL_GQ0_VARIANTS
The total number of variants in a particular sample that have a GQ score of 0.
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TOTAL_HET_DEPTH
public long TOTAL_HET_DEPTH
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
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Method Detail
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getFileExtension
public static String getFileExtension()
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calculateDerivedFields
public void calculateDerivedFields()
Description copied from class:MergeableMetricBase
Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated withNoMergingKeepsValue
.- Overrides:
calculateDerivedFields
in classCollectVariantCallingMetrics.VariantCallingSummaryMetrics
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calculateFromDerivedFields
public void calculateFromDerivedFields()
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