CollectVariantCallingMetrics.VariantCallingDetailMetrics
public static class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
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 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 fraction of high confidence SNPs in dbSNP
|
float |
PCT_DBSNP_INDELS |
The fraction 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 | Description |
---|---|
VariantCallingSummaryMetrics() |
Modifier and Type | Method | Description |
---|---|---|
static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> |
foldInto(T target,
Collection<T> metrics) |
|
static String |
getFileExtension() |
|
void |
updateDerivedValuesInPlace() |
public long TOTAL_SNPS
public long NUM_IN_DB_SNP
public long NOVEL_SNPS
public long FILTERED_SNPS
public float PCT_DBSNP
public double DBSNP_TITV
public double NOVEL_TITV
public long TOTAL_INDELS
public long NOVEL_INDELS
public long FILTERED_INDELS
public float PCT_DBSNP_INDELS
public long NUM_IN_DB_SNP_INDELS
public double DBSNP_INS_DEL_RATIO
public double NOVEL_INS_DEL_RATIO
public double TOTAL_MULTIALLELIC_SNPS
public double NUM_IN_DB_SNP_MULTIALLELIC
public double TOTAL_COMPLEX_INDELS
public double NUM_IN_DB_SNP_COMPLEX_INDELS
public double SNP_REFERENCE_BIAS
public long NUM_SINGLETONS
public static String getFileExtension()
public void updateDerivedValuesInPlace()
public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target, Collection<T> metrics)