public static class CollectVariantCallingMetrics.VariantCallingDetailMetrics extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue| Modifier and Type | Field | Description |
|---|---|---|
double |
HET_HOMVAR_RATIO |
(count of hets)/(count of homozygous non-ref) for this sample
|
double |
PCT_GQ0_VARIANTS |
The percentage of variants in a particular sample that have a GQ score of 0.
|
String |
SAMPLE_ALIAS |
The name of the sample being assayed
|
long |
TOTAL_GQ0_VARIANTS |
The total number of variants in a particular sample that have a GQ score of 0.
|
long |
TOTAL_HET_DEPTH |
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
|
DBSNP_INS_DEL_RATIO, DBSNP_TITV, FILTERED_INDELS, FILTERED_SNPS, NOVEL_INDELS, NOVEL_INS_DEL_RATIO, NOVEL_SNPS, NOVEL_TITV, NUM_IN_DB_SNP, NUM_IN_DB_SNP_COMPLEX_INDELS, NUM_IN_DB_SNP_INDELS, NUM_IN_DB_SNP_MULTIALLELIC, NUM_SINGLETONS, PCT_DBSNP, PCT_DBSNP_INDELS, SNP_REFERENCE_BIAS, TOTAL_COMPLEX_INDELS, TOTAL_INDELS, TOTAL_MULTIALLELIC_SNPS, TOTAL_SNPS| Constructor | Description |
|---|---|
VariantCallingDetailMetrics() |
| Modifier and Type | Method | Description |
|---|---|---|
void |
calculateDerivedFields() |
placeholder method that will calculate the derived fields from the other ones.
|
void |
calculateFromDerivedFields() |
|
static String |
getFileExtension() |
calculateFromDerivedFields, foldIntocanMerge, merge, merge, mergeIfCanpublic String SAMPLE_ALIAS
public double HET_HOMVAR_RATIO
public double PCT_GQ0_VARIANTS
public long TOTAL_GQ0_VARIANTS
public long TOTAL_HET_DEPTH
public static String getFileExtension()
public void calculateDerivedFields()
MergeableMetricBasecalculateDerivedFields in class CollectVariantCallingMetrics.VariantCallingSummaryMetricspublic void calculateFromDerivedFields()