Package picard.vcf
Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- 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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- 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
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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
DBSNP_INS_DEL_RATIO
The Insertion/Deletion ratio of the indel calls made at dbSNP sitesdouble
DBSNP_TITV
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP siteslong
FILTERED_INDELS
The number of indels that are filteredlong
FILTERED_SNPS
The number of SNPs that are filteredlong
NOVEL_INDELS
The number of passing indels called that were not found in dbSNPdouble
NOVEL_INS_DEL_RATIO
The Insertion/Deletion ratio of the indel calls made at non-dbSNP siteslong
NOVEL_SNPS
The number of passing bi-allelic SNPS called that were not found in dbSNPdouble
NOVEL_TITV
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP siteslong
NUM_IN_DB_SNP
The number of passing bi-allelic SNPs found in dbSNPdouble
NUM_IN_DB_SNP_COMPLEX_INDELS
The number of passing complex indels found in dbSNPlong
NUM_IN_DB_SNP_INDELS
The number of passing indels found in dbSNPdouble
NUM_IN_DB_SNP_MULTIALLELIC
The number of passing multi-allelic SNPs found in dbSNPlong
NUM_SINGLETONS
For summary metrics, the number of variants that appear in only one sample.float
PCT_DBSNP
The fraction of passing bi-allelic SNPs in dbSNPfloat
PCT_DBSNP_INDELS
The fraction of passing indels in dbSNPdouble
SNP_REFERENCE_BIAS
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.double
TOTAL_COMPLEX_INDELS
The number of passing complex indel calls that were examinedlong
TOTAL_INDELS
The number of passing indel calls that were examineddouble
TOTAL_MULTIALLELIC_SNPS
The number of passing multi-allelic SNP calls that were examinedlong
TOTAL_SNPS
The number of passing bi-allelic SNPs calls (i.e.
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Constructor Summary
Constructors Constructor Description VariantCallingSummaryMetrics()
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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(long totalHetDepth)
static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics>
voidfoldInto(T target, Collection<T> metrics)
static String
getFileExtension()
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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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TOTAL_SNPS
public long TOTAL_SNPS
The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined
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NUM_IN_DB_SNP
public long NUM_IN_DB_SNP
The number of passing bi-allelic SNPs found in dbSNP
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NOVEL_SNPS
public long NOVEL_SNPS
The number of passing bi-allelic SNPS called that were not found in dbSNP
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FILTERED_SNPS
public long FILTERED_SNPS
The number of SNPs that are filtered
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PCT_DBSNP
public float PCT_DBSNP
The fraction of passing bi-allelic SNPs in dbSNP
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DBSNP_TITV
public double DBSNP_TITV
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
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NOVEL_TITV
public double NOVEL_TITV
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
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TOTAL_INDELS
public long TOTAL_INDELS
The number of passing indel calls that were examined
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NOVEL_INDELS
public long NOVEL_INDELS
The number of passing indels called that were not found in dbSNP
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FILTERED_INDELS
public long FILTERED_INDELS
The number of indels that are filtered
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PCT_DBSNP_INDELS
public float PCT_DBSNP_INDELS
The fraction of passing indels in dbSNP
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NUM_IN_DB_SNP_INDELS
public long NUM_IN_DB_SNP_INDELS
The number of passing indels found in dbSNP
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DBSNP_INS_DEL_RATIO
public double DBSNP_INS_DEL_RATIO
The Insertion/Deletion ratio of the indel calls made at dbSNP sites
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NOVEL_INS_DEL_RATIO
public double NOVEL_INS_DEL_RATIO
The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
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TOTAL_MULTIALLELIC_SNPS
public double TOTAL_MULTIALLELIC_SNPS
The number of passing multi-allelic SNP calls that were examined
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NUM_IN_DB_SNP_MULTIALLELIC
public double NUM_IN_DB_SNP_MULTIALLELIC
The number of passing multi-allelic SNPs found in dbSNP
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TOTAL_COMPLEX_INDELS
public double TOTAL_COMPLEX_INDELS
The number of passing complex indel calls that were examined
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NUM_IN_DB_SNP_COMPLEX_INDELS
public double NUM_IN_DB_SNP_COMPLEX_INDELS
The number of passing complex indels found in dbSNP
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SNP_REFERENCE_BIAS
public double SNP_REFERENCE_BIAS
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
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NUM_SINGLETONS
public long NUM_SINGLETONS
For 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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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 classMergeableMetricBase
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calculateFromDerivedFields
public void calculateFromDerivedFields(long totalHetDepth)
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foldInto
public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target, Collection<T> metrics)
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