Class MendelianViolationMetrics


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

      • 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 Detail

      • MendelianViolationMetrics

        public MendelianViolationMetrics()
    • Method Detail

      • 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