public class MendelianViolationMetrics extends MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
Modifier and Type | Field and Description |
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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 and Description |
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MendelianViolationMetrics() |
Modifier and Type | Method and Description |
---|---|
void |
calculateDerivedFields()
placeholder method that will calculate the derived fields from the other ones.
|
static String |
getExtension() |
canMerge, merge, merge, mergeIfCan
public String FAMILY_ID
public String MOTHER
public String FATHER
public String OFFSPRING
public Sex OFFSPRING_SEX
public long NUM_VARIANT_SITES
public long NUM_DIPLOID_DENOVO
public long NUM_HOMVAR_HOMVAR_HET
public long NUM_HOMREF_HOMVAR_HOM
public long NUM_HOM_HET_HOM
public long NUM_HAPLOID_DENOVO
public long NUM_HAPLOID_OTHER
public long NUM_OTHER
public long TOTAL_MENDELIAN_VIOLATIONS
public static String getExtension()
public void calculateDerivedFields()
MergeableMetricBase
calculateDerivedFields
in class MergeableMetricBase