Package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
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ClassDescriptionThis is a marker interface used to indicate which annotations are allele-specific.A class to encapsulate the raw data for allele-specific classes compatible with the ReducibleAnnotation interfaceAllele-specific rank Sum Test of REF versus ALT base quality scoresAllele-specific strand bias estimated using Fisher's Exact Test *Allele-specific likelihood-based test for the inbreeding among samplesAllele specific Rank Sum Test for mapping qualities of REF versus ALT readsAllele-specific call confidence normalized by depth of sample reads supporting the alleleAllele-specific implementation of rank sum test annotationsAllele-specific Rank Sum Test for relative positioning of REF versus ALT allele within readsAllele-specific Root Mean Square of the mapping quality of reads across all samples.This is a marker interface used to indicate which annotations are "Standard" and allele-specific.Allele-specific implementation of strand bias annotationsAllele-specific strand bias estimated by the Symmetric Odds Ratio testAn interface for annotations that are calculated using raw data across samples, rather than the median (or median of median) of samples values The Raw annotation keeps some summary (one example might be a histogram of the raw values for each sample) of the individual sample (or allele) level annotation.A class to encapsulate the raw data for classes compatible with the ReducibleAnnotation interfaceCommon strand bias utilities used by allele specific strand bias annotators