Class MendelianViolationMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.vcf.MendelianViolations.MendelianViolationMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class MendelianViolationMetrics extends MergeableMetricBase
Describes the type and number of mendelian violations found within a Trio.
  • Field Details

    • FAMILY_ID

      public String FAMILY_ID
      The family ID assigned to the trio for which these metrics are calculated.
    • MOTHER

      public String MOTHER
      The ID of the mother within the trio.
    • FATHER

      public String FATHER
      The ID of the father within the trio.
    • OFFSPRING

      public String OFFSPRING
      The ID of the offspring within the trio.
    • OFFSPRING_SEX

      public Sex OFFSPRING_SEX
      The sex of the offspring.
    • NUM_VARIANT_SITES

      public long NUM_VARIANT_SITES
      The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
    • NUM_DIPLOID_DENOVO

      public long NUM_DIPLOID_DENOVO
      The number of diploid sites at which a potential de-novo mutation was observed (i.e. both parents are hom-ref, offspring is not hom-ref.
    • NUM_HOMVAR_HOMVAR_HET

      public long NUM_HOMVAR_HOMVAR_HET
      The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
    • NUM_HOMREF_HOMVAR_HOM

      public long NUM_HOMREF_HOMVAR_HOM
      The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
    • NUM_HOM_HET_HOM

      public long NUM_HOM_HET_HOM
      The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
    • NUM_HAPLOID_DENOVO

      public long NUM_HAPLOID_DENOVO
      The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
    • NUM_HAPLOID_OTHER

      public long NUM_HAPLOID_OTHER
      The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
    • NUM_OTHER

      public long NUM_OTHER
      The number of otherwise unclassified events.
    • TOTAL_MENDELIAN_VIOLATIONS

      public long TOTAL_MENDELIAN_VIOLATIONS
      The total of all mendelian violations observed.
  • Constructor Details

    • MendelianViolationMetrics

      public MendelianViolationMetrics()
  • Method Details

    • getExtension

      public static String getExtension()
    • 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