GenomicsDB
GenomicsDB Docs
Overview
Concepts + Terminology
Supported Storage
Local / Cluster
Cloud
Building + Installing
Bash
Docker
CLI Tools
Import / ETL
VCF/gVCF
Organizing your data
CSV
Preliminaries
CSV format
Example
Special fields
Organizing your data
Multi-node setup
Common Issues
API Docs
APIs
Overview
GenomicsDB Protobuf Documentation
genomicsdb_callsets_mapping.proto
CallsetMappingPB
SampleIDToTileDBIDMap
genomicsdb_coordinates.proto
ContigInterval
ContigPosition
GenomicsDBColumn
GenomicsDBColumnInterval
GenomicsDBColumnOrInterval
TileDBColumnInterval
genomicsdb_export_config.proto
AnnotationSource
ExportConfiguration
GenomicsDBColumnOrIntervalList
QueryConfiguration
RowRange
RowRangeList
SparkConfig
genomicsdb_import_config.proto
ImportConfiguration
Partition
genomicsdb_vid_mapping.proto
Chromosome
FieldLengthDescriptorComponentPB
GenomicsDBFieldInfo
VidMappingPB
Scalar Value Types
C++
API Reference
C++ Query Interface
Python
API Reference
genomicsdb module
Java
API Reference
Java Import Package
Java Query Package
CLI Tools
vcf2genomicsdb_init
vcf2genomicsdb
gt_mpi_gather
create_genomicsdb_workspace
consolidate_genomicsdb_array
vcf_histogram
vcfdiff
Examples
Example Python notebook connecting to GenomicsDB on Azure Blob storage
Import / ETL Examples
Using GenomicsDB with GATK
GenomicsDB
Index
Index
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GenomicsDB (C++ class)
GenomicsDB::GenomicsDB (C++ function)
,
[1]
GenomicsDB::~GenomicsDB (C++ function)
O
org::genomicsdb::model::BatchCompletionCallbackFunctionArgument (C++ class)
org::genomicsdb::model::ImportConfig (C++ class)
org::genomicsdb::model::ImportConfig::Func (C++ class)
org::genomicsdb::reader::GenomicsDBQuery (C++ class)
org::genomicsdb::reader::GenomicsDBQuery::Interval (C++ class)
org::genomicsdb::reader::GenomicsDBQuery::Pair (C++ class)
org::genomicsdb::reader::GenomicsDBQuery::VariantCall (C++ class)
P
PhonyNameDueToError::columnPartitionIterator (C++ function)
PhonyNameDueToError::doSingleImport (C++ function)
PhonyNameDueToError::executeImport (C++ function)
PhonyNameDueToError::getHeader (C++ function)
PhonyNameDueToError::getNumExhaustedBufferStreams (C++ function)
PhonyNameDueToError::getSequenceNames (C++ function)
PhonyNameDueToError::isDone (C++ function)
PhonyNameDueToError::iterator (C++ function)
PhonyNameDueToError::setupGenomicsDBImporter (C++ function)
PhonyNameDueToError::write (C++ function)