Package picard.vcf.MendelianViolations
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.
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
-
-
Field Summary
Fields Modifier and Type Field Description String
FAMILY_ID
The family ID assigned to the trio for which these metrics are calculated.String
FATHER
The ID of the father within the trio.String
MOTHER
The ID of the mother within the trio.long
NUM_DIPLOID_DENOVO
The number of diploid sites at which a potential de-novo mutation was observed (i.e.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.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.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.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.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.long
NUM_OTHER
The number of otherwise unclassified events.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.String
OFFSPRING
The ID of the offspring within the trio.Sex
OFFSPRING_SEX
The sex of the offspring.long
TOTAL_MENDELIAN_VIOLATIONS
The total of all mendelian violations observed.
-
Constructor Summary
Constructors Constructor Description MendelianViolationMetrics()
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calculateDerivedFields()
Placeholder method that will calculate the derived fields from the other ones.static String
getExtension()
-
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
-
-
-
-
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.
-
-
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 withNoMergingKeepsValue
.- Overrides:
calculateDerivedFields
in classMergeableMetricBase
-
-