CollectVariantCallingMetrics.VariantCallingSummaryMetrics (picard 2.18.2 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.MergeableMetricBase
  - - picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics

Direct Known Subclasses:

CollectVariantCallingMetrics.VariantCallingDetailMetrics

Enclosing class:

CollectVariantCallingMetrics
```
public static class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
extends MergeableMetricBase
```
A collection of metrics relating to snps and indels within a variant-calling file (VCF).

Nested Class Summary
- Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
  MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

Field Summary

Fields
Modifier and Type	Field	Description
`double`	`DBSNP_INS_DEL_RATIO`	The Insertion/Deletion ratio of the indel calls made at dbSNP sites
`double`	`DBSNP_TITV`	The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
`long`	`FILTERED_INDELS`	The number of indels that are filtered
`long`	`FILTERED_SNPS`	The number of SNPs that are filtered
`long`	`NOVEL_INDELS`	The number of passing indels called that were not found in dbSNP
`double`	`NOVEL_INS_DEL_RATIO`	The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
`long`	`NOVEL_SNPS`	The number of passing bi-allelic SNPS called that were not found in dbSNP
`double`	`NOVEL_TITV`	The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
`long`	`NUM_IN_DB_SNP`	The number of passing bi-allelic SNPs found in dbSNP
`double`	`NUM_IN_DB_SNP_COMPLEX_INDELS`	The number of passing complex indels found in dbSNP
`long`	`NUM_IN_DB_SNP_INDELS`	The number of passing indels found in dbSNP
`double`	`NUM_IN_DB_SNP_MULTIALLELIC`	The number of passing multi-allelic SNPs found in dbSNP
`long`	`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 dbSNP
`float`	`PCT_DBSNP_INDELS`	The fraction of passing indels in dbSNP
`double`	`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 examined
`long`	`TOTAL_INDELS`	The number of passing indel calls that were examined
`double`	`TOTAL_MULTIALLELIC_SNPS`	The number of passing multi-allelic SNP calls that were examined
`long`	`TOTAL_SNPS`	The number of passing bi-allelic SNPs calls (i.e.

Constructor Summary

Constructors
Constructor Description

VariantCallingSummaryMetrics()

Constructors
Constructor	Description
`VariantCallingSummaryMetrics()`

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> void`	`foldInto(T target, Collection<T> metrics)`
`static String`	`getFileExtension()`

Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan

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
  - TOTAL_SNPS
```
public long TOTAL_SNPS
```
    The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined
  - NUM_IN_DB_SNP
```
public long NUM_IN_DB_SNP
```
    The number of passing bi-allelic SNPs found in dbSNP
  - NOVEL_SNPS
```
public long NOVEL_SNPS
```
    The number of passing bi-allelic SNPS called that were not found in dbSNP
  - FILTERED_SNPS
```
public long FILTERED_SNPS
```
    The number of SNPs that are filtered
  - PCT_DBSNP
```
public float PCT_DBSNP
```
    The fraction of passing bi-allelic SNPs in dbSNP
  - DBSNP_TITV
```
public double DBSNP_TITV
```
    The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
  - NOVEL_TITV
```
public double NOVEL_TITV
```
    The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
  - TOTAL_INDELS
```
public long TOTAL_INDELS
```
    The number of passing indel calls that were examined
  - NOVEL_INDELS
```
public long NOVEL_INDELS
```
    The number of passing indels called that were not found in dbSNP
  - FILTERED_INDELS
```
public long FILTERED_INDELS
```
    The number of indels that are filtered
  - PCT_DBSNP_INDELS
```
public float PCT_DBSNP_INDELS
```
    The fraction of passing indels in dbSNP
  - NUM_IN_DB_SNP_INDELS
```
public long NUM_IN_DB_SNP_INDELS
```
    The number of passing indels found in dbSNP
  - DBSNP_INS_DEL_RATIO
```
public double DBSNP_INS_DEL_RATIO
```
    The Insertion/Deletion ratio of the indel calls made at dbSNP sites
  - NOVEL_INS_DEL_RATIO
```
public double NOVEL_INS_DEL_RATIO
```
    The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
  - TOTAL_MULTIALLELIC_SNPS
```
public double TOTAL_MULTIALLELIC_SNPS
```
    The number of passing multi-allelic SNP calls that were examined
  - NUM_IN_DB_SNP_MULTIALLELIC
```
public double NUM_IN_DB_SNP_MULTIALLELIC
```
    The number of passing multi-allelic SNPs found in dbSNP
  - TOTAL_COMPLEX_INDELS
```
public double TOTAL_COMPLEX_INDELS
```
    The number of passing complex indel calls that were examined
  - NUM_IN_DB_SNP_COMPLEX_INDELS
```
public double NUM_IN_DB_SNP_COMPLEX_INDELS
```
    The number of passing complex indels found in dbSNP
  - SNP_REFERENCE_BIAS
```
public double SNP_REFERENCE_BIAS
```
    The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
  - 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.
- Constructor Detail
  - VariantCallingSummaryMetrics
```
public VariantCallingSummaryMetrics()
```
- Method Detail
  - getFileExtension
```
public static String getFileExtension()
```
  - 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 base classes should consider calling super.calculateDerivedFields() as well.
    
    Overrides:
    
    calculateDerivedFields in class MergeableMetricBase
  - calculateFromDerivedFields
```
public void calculateFromDerivedFields(long totalHetDepth)
```
  - foldInto
```
public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target,
                                                                                                  Collection<T> metrics)
```

Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

Field Summary

Constructor Summary

Method Summary

Methods inherited from class picard.analysis.MergeableMetricBase

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

TOTAL_SNPS

NUM_IN_DB_SNP

NOVEL_SNPS

FILTERED_SNPS

PCT_DBSNP

DBSNP_TITV

NOVEL_TITV

TOTAL_INDELS

NOVEL_INDELS

FILTERED_INDELS

PCT_DBSNP_INDELS

NUM_IN_DB_SNP_INDELS

DBSNP_INS_DEL_RATIO

NOVEL_INS_DEL_RATIO

TOTAL_MULTIALLELIC_SNPS

NUM_IN_DB_SNP_MULTIALLELIC

TOTAL_COMPLEX_INDELS

NUM_IN_DB_SNP_COMPLEX_INDELS

SNP_REFERENCE_BIAS

NUM_SINGLETONS

Constructor Detail

VariantCallingSummaryMetrics

Method Detail

getFileExtension

calculateDerivedFields

calculateFromDerivedFields

foldInto