Package org.broadinstitute.hellbender.tools.walkers.annotator
package org.broadinstitute.hellbender.tools.walkers.annotator
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ClassDescriptionVariant allele fraction for each sample.An annotation group is a set of annotation that have something in common and should be added at the same time.Adds the strand bias table annotation for use in mutect filtersMedian base quality of bases supporting each allele.Rank Sum Test of REF versus ALT base quality scoresCounts and frequency of alleles in called genotypesRank Sum Test for hard-clipped bases on REF versus ALT readsApply a read-based annotation that reports the number of Ns seen at a given site.Total depth of coverage per sample and over all samples.Depth of coverage of each allele per sampleDepth of informative coverage for each sample.Phred-scaled p-value for exact test of excess heterozygosity.For each sample and for each allele a list feature vectors of supporting reads In order to reduce the number of delimiter characters, we flatten featurized reads.Strand bias estimated using Fisher's Exact TestFragment depth of coverage of each allele per sampleMedian fragment length of reads supporting each allele.Represents an annotation that is computed for a single genotype.Summarize genotype statistics from all samples at the site levelSet of annotations meant to be reflective of HaplotypeFiltering operations that were applied in FlowBased HaplotypeCaller.A class containing utility methods used in the calculation of annotations related to cohort heterozygosity, e.g.Likelihood-based test for the consanguinuity among samplesAnnotations relevant to the INFO field of the variant file (ie annotations for sites).FORMAT annotations that look at more inputs than regular annotationsINFO annotations that look at more inputs than regular annotationsRank Sum Test of per-read likelihoods of REF versus ALT readsMedian mapping quality of reads supporting each alt allele.Rank Sum Test for mapping qualities of REF versus ALT readsCount of all reads with MAPQ = 0 across all samplesCount of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate allelesOriginal Alignment annotation counts the number of alt reads where the original alignment contig doesn't match the current alignment contigA common interface for handling annotations that require pedigree file information either in the form of explicitly selected founderIDs or in the form of an imported pedigreeFile.Apply an annotation based on aggregation data from all reads supporting each allele.Existence of a de novo mutation in at least one of the given familiesVariant confidence normalized by unfiltered depth of variant samplesAbstract root for all RankSum based annotationsINFO level annotation of the counts of genotypes with respect to the reference allele.Median distance of variant starts from ends of reads supporting each alt allele.Rank Sum Test for relative positioning of REF versus ALT alleles within readsLocal reference context at a variant position.Root Mean Square of the mapping quality of reads across all samples.List samples that are non-reference at a given variant siteThis is a marker interface used to indicate which annotations are "Standard".This is a marker interface used to indicate which annotations are "Standard" for the HaplotypeCaller only.This is a marker interface used to indicate which annotations are "Standard" for Mutect2 only.Number of forward and reverse reads that support REF and ALT allelesClass of tests to detect strand bias.Strand bias estimated by the Symmetric Odds Ratio testTandem repeat unit composition and counts per alleleFinds a lower bound on the number of unique reads at a locus that support a non-reference allele.Interface of all variant annotations.Annotate variant calls with context informationThe class responsible for computing annotations for variants.A container object for storing the objects necessary for carrying over expression annotations.Annotate the ID field and attribute overlap FLAGs for a VariantContext against a FeatureContext or a list of VariantContexts.