Package org.broadinstitute.hellbender.tools.genomicsdb

package org.broadinstitute.hellbender.tools.genomicsdb
  • Classes
    Class
    Description
    GATKGenomicsDBUtils
    Utility class containing various methods for working with GenomicsDB Contains code to modify the GenomicsDB import input using the Protobuf API References: GenomicsDB Protobuf structs: https://github.com/GenomicsDB/GenomicsDB/blob/master/src/resources/genomicsdb_vid_mapping.proto Protobuf generated Java code guide: https://developers.google.com/protocol-buffers/docs/javatutorial#the-protocol-buffer-api https://developers.google.com/protocol-buffers/docs/reference/java-generated
    GenomicsDBArgumentCollection
     
    GenomicsDBConstants
    Constants related to GenomicsDB
    GenomicsDBImport
    Import single-sample GVCFs into GenomicsDB before joint genotyping.
    GenomicsDBOptions
    Encapsulates the GenomicsDB-specific options relevant to the FeatureDataSource
    SampleNameMap
    A class to hold the mappings of sample names to VCF / VCF index paths.