Package picard.vcf
Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- Direct Known Subclasses:
CollectVariantCallingMetrics.VariantCallingDetailMetrics
- Enclosing class:
- CollectVariantCallingMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
extends MergeableMetricBase
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
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Nested Class Summary
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
FieldsModifier and TypeFieldDescriptiondouble
The Insertion/Deletion ratio of the indel calls made at dbSNP sitesdouble
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP siteslong
The number of indels that are filteredlong
The number of SNPs that are filteredlong
The number of passing indels called that were not found in dbSNPdouble
The Insertion/Deletion ratio of the indel calls made at non-dbSNP siteslong
The number of passing bi-allelic SNPS called that were not found in dbSNPdouble
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP siteslong
The number of passing bi-allelic SNPs found in dbSNPdouble
The number of passing complex indels found in dbSNPlong
The number of passing indels found in dbSNPdouble
The number of passing multi-allelic SNPs found in dbSNPlong
For summary metrics, the number of variants that appear in only one sample.float
The fraction of passing bi-allelic SNPs in dbSNPfloat
The fraction of passing indels in dbSNPdouble
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.double
The number of passing complex indel calls that were examinedlong
The number of passing indel calls that were examineddouble
The number of passing multi-allelic SNP calls that were examinedlong
The number of passing bi-allelic SNPs calls (i.e. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.void
calculateFromDerivedFields
(long totalHetDepth) static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics>
voidfoldInto
(T target, Collection<T> metrics) static String
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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TOTAL_SNPS
public long TOTAL_SNPSThe number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined -
NUM_IN_DB_SNP
public long NUM_IN_DB_SNPThe number of passing bi-allelic SNPs found in dbSNP -
NOVEL_SNPS
public long NOVEL_SNPSThe number of passing bi-allelic SNPS called that were not found in dbSNP -
FILTERED_SNPS
public long FILTERED_SNPSThe number of SNPs that are filtered -
PCT_DBSNP
public float PCT_DBSNPThe fraction of passing bi-allelic SNPs in dbSNP -
DBSNP_TITV
public double DBSNP_TITVThe Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites -
NOVEL_TITV
public double NOVEL_TITVThe Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites -
TOTAL_INDELS
public long TOTAL_INDELSThe number of passing indel calls that were examined -
NOVEL_INDELS
public long NOVEL_INDELSThe number of passing indels called that were not found in dbSNP -
FILTERED_INDELS
public long FILTERED_INDELSThe number of indels that are filtered -
PCT_DBSNP_INDELS
public float PCT_DBSNP_INDELSThe fraction of passing indels in dbSNP -
NUM_IN_DB_SNP_INDELS
public long NUM_IN_DB_SNP_INDELSThe number of passing indels found in dbSNP -
DBSNP_INS_DEL_RATIO
public double DBSNP_INS_DEL_RATIOThe Insertion/Deletion ratio of the indel calls made at dbSNP sites -
NOVEL_INS_DEL_RATIO
public double NOVEL_INS_DEL_RATIOThe Insertion/Deletion ratio of the indel calls made at non-dbSNP sites -
TOTAL_MULTIALLELIC_SNPS
public double TOTAL_MULTIALLELIC_SNPSThe number of passing multi-allelic SNP calls that were examined -
NUM_IN_DB_SNP_MULTIALLELIC
public double NUM_IN_DB_SNP_MULTIALLELICThe number of passing multi-allelic SNPs found in dbSNP -
TOTAL_COMPLEX_INDELS
public double TOTAL_COMPLEX_INDELSThe number of passing complex indel calls that were examined -
NUM_IN_DB_SNP_COMPLEX_INDELS
public double NUM_IN_DB_SNP_COMPLEX_INDELSThe number of passing complex indels found in dbSNP -
SNP_REFERENCE_BIAS
public double SNP_REFERENCE_BIASThe rate at which reference bases are observed at ref/alt heterozygous SNP sites. -
NUM_SINGLETONS
public long NUM_SINGLETONSFor summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample.
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Constructor Details
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VariantCallingSummaryMetrics
public VariantCallingSummaryMetrics()
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Method Details
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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 classMergeableMetricBase
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calculateFromDerivedFields
public void calculateFromDerivedFields(long totalHetDepth) -
foldInto
public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target, Collection<T> metrics)
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