CollectVariantCallingMetrics.VariantCallingSummaryMetrics (PICARD JDK API Documentation)

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

Direct Known Subclasses:

CollectVariantCallingMetrics.VariantCallingDetailMetrics

Enclosing class:

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

Field Summary

Fields
Modifier and Type	Field and 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 SNP calls made at dbSNP sites
`long`	`FILTERED_INDELS` The number of indels that are also filtered
`long`	`FILTERED_SNPS` The number of SNPs that are also filtered
`long`	`NOVEL_INDELS` The number of high confidence 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 high confidence SNPS called that were not found in dbSNP
`double`	`NOVEL_TITV` The Transition/Transversion ratio of the SNP calls made at non-dbSNP sites
`long`	`NUM_IN_DB_SNP` The number of high confidence SNPs found in dbSNP
`double`	`NUM_IN_DB_SNP_COMPLEX_INDELS` The number of high confidence complex Indels found in dbSNP
`long`	`NUM_IN_DB_SNP_INDELS` The number of high confidence Indels found in dbSNP
`double`	`NUM_IN_DB_SNP_MULTIALLELIC` The number of high confidence multiallelic SNPs found in dbSNP
`long`	`NUM_SINGLETONS` For summary metrics, the number of variants that appear in only one sample.
`float`	`PCT_DBSNP` The percentage of high confidence SNPs in dbSNP
`float`	`PCT_DBSNP_INDELS` The percentage of high confidence 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 high confidence complex Indel calls that were examined
`long`	`TOTAL_INDELS` The number of high confidence Indel calls that were examined
`double`	`TOTAL_MULTIALLELIC_SNPS` The number of high confidence multiallelic SNP calls that were examined
`long`	`TOTAL_SNPS` The number of high confidence SNPs calls (i.e.

Constructor Summary

Constructors
Constructor and Description

VariantCallingSummaryMetrics()

Constructors
Constructor and Description
`VariantCallingSummaryMetrics()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void`	`foldInto(T target, java.util.Collection<T> metrics)`
`static java.lang.String`	`getFileExtension()`
`void`	`updateDerivedValuesInPlace()`

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 high confidence SNPs calls (i.e. non-reference genotypes) that were examined
  - NUM_IN_DB_SNP
```
public long NUM_IN_DB_SNP
```
    The number of high confidence SNPs found in dbSNP
  - NOVEL_SNPS
```
public long NOVEL_SNPS
```
    The number of high confidence SNPS called that were not found in dbSNP
  - FILTERED_SNPS
```
public long FILTERED_SNPS
```
    The number of SNPs that are also filtered
  - PCT_DBSNP
```
public float PCT_DBSNP
```
    The percentage of high confidence SNPs in dbSNP
  - DBSNP_TITV
```
public double DBSNP_TITV
```
    The Transition/Transversion ratio of the SNP calls made at dbSNP sites
  - NOVEL_TITV
```
public double NOVEL_TITV
```
    The Transition/Transversion ratio of the SNP calls made at non-dbSNP sites
  - TOTAL_INDELS
```
public long TOTAL_INDELS
```
    The number of high confidence Indel calls that were examined
  - NOVEL_INDELS
```
public long NOVEL_INDELS
```
    The number of high confidence Indels called that were not found in dbSNP
  - FILTERED_INDELS
```
public long FILTERED_INDELS
```
    The number of indels that are also filtered
  - PCT_DBSNP_INDELS
```
public float PCT_DBSNP_INDELS
```
    The percentage of high confidence Indels in dbSNP
  - NUM_IN_DB_SNP_INDELS
```
public long NUM_IN_DB_SNP_INDELS
```
    The number of high confidence 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 high confidence multiallelic SNP calls that were examined
  - NUM_IN_DB_SNP_MULTIALLELIC
```
public double NUM_IN_DB_SNP_MULTIALLELIC
```
    The number of high confidence multiallelic SNPs found in dbSNP
  - TOTAL_COMPLEX_INDELS
```
public double TOTAL_COMPLEX_INDELS
```
    The number of high confidence complex Indel calls that were examined
  - NUM_IN_DB_SNP_COMPLEX_INDELS
```
public double NUM_IN_DB_SNP_COMPLEX_INDELS
```
    The number of high confidence 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 java.lang.String getFileExtension()
```
  - updateDerivedValuesInPlace
```
public void updateDerivedValuesInPlace()
```
  - foldInto
```
public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target,
                                                                                                  java.util.Collection<T> metrics)
```

Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics

Field Summary

Constructor Summary

Method Summary

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

updateDerivedValuesInPlace

foldInto