Package org.broadinstitute.hellbender.tools.funcotator
package org.broadinstitute.hellbender.tools.funcotator
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ClassDescriptionClass for managing aliases and querying
Funcotationto determine fields.Enum to hold the amino acids and their standard codons.Converts an annotated interval representing a segment to a variant context.An abstract class to allow for the creation of aFuncotationfor a given data source.Filter variants based on clinically-significant Funcotations.The allele frequency data source that was used when Funcotating the input VCF.The version of the Human Genome reference which was used when Funcotating the input VCF.Simple struct container class for the 5'/3' flank settings.Perform functional annotation on a segment file (tsv).Abstract class representing aFuncotatorannotation.A linked map of transcript IDs to funcotations.Funcotator (FUNCtional annOTATOR) analyzes given variants for their function (as retrieved from a set of data sources) and produces the analysis in a specified output file.Class to store argument definitions specific toFuncotator.An enum to handle the different types of input files for data sources.The file format of the output file.FuncotatorDataSourceDownloaderis a tool to download the latest data sources forFuncotator.Class that performs functional annotation of variants.A type to keep track of different specific genuses.Class representing exceptions that arise when trying to create a coding sequence for a variant:An abstract class to allow for writing output for the Funcotator.Class representing the change in the protein sequence for a specific reference/alternate allele pair in a variant.A simple data object to hold a comparison between a reference sequence and an alternate allele.Class to represent a strand-correctedAllele.Simple container class to represent bases that have been corrected for strandedness already.The manner to select a single transcript from a set of transcripts to report as the "best" or main transcript.