Package picard.vcf

Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
Direct Known Subclasses:
CollectVariantCallingMetrics.VariantCallingDetailMetrics
Enclosing class:
CollectVariantCallingMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectVariantCallingMetrics.VariantCallingSummaryMetrics extends MergeableMetricBase
A collection of metrics relating to snps and indels within a variant-calling file (VCF).

  • Field Details

    • 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 Details

    • VariantCallingSummaryMetrics

      public VariantCallingSummaryMetrics()

  • 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 MergeableMetricBase

    • calculateFromDerivedFields

      public void calculateFromDerivedFields(long totalHetDepth)

    • foldInto

      public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto(T target, Collection<T> metrics)