GenomicsDB
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GenomicsDB Docs
Overview
Concepts + Terminology
Supported Storage
Local / Cluster
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Bash
Docker
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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
APIs
genomicsdb module
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genomicsdb module
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