Package picard.vcf

Class CollectVariantCallingMetrics.VariantCallingDetailMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
Enclosing class:
CollectVariantCallingMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectVariantCallingMetrics.VariantCallingDetailMetrics extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
  • Field Details

    • SAMPLE_ALIAS

      public String SAMPLE_ALIAS
      The name of the sample being assayed
    • HET_HOMVAR_RATIO

      public double HET_HOMVAR_RATIO
      (count of hets)/(count of homozygous non-ref) for this sample
    • PCT_GQ0_VARIANTS

      public double PCT_GQ0_VARIANTS
      The percentage of variants in a particular sample that have a GQ score of 0.
    • TOTAL_GQ0_VARIANTS

      public long TOTAL_GQ0_VARIANTS
      The total number of variants in a particular sample that have a GQ score of 0.
    • TOTAL_HET_DEPTH

      public long TOTAL_HET_DEPTH
      total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
  • Constructor Details

    • VariantCallingDetailMetrics

      public VariantCallingDetailMetrics()
  • Method Details

    • 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 derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
      Overrides:
      calculateDerivedFields in class CollectVariantCallingMetrics.VariantCallingSummaryMetrics
    • calculateFromDerivedFields

      public void calculateFromDerivedFields()