Data repository¶

Each GA4GH server represents a repository of information. This repository consists of the reference sets, datasets, readgroup sets, variant sets etc. in the server’s data model and may contain data from many different unrelated projects. The server administrator defines and manages this repository using the ga4gh_repo command line interface, which provides commands to manage all of the objects represented by a GA4GH server.

The information about the objects in the GA4GH data model is stored in an SQL database, called the “registry DB” or “registry”. The registry DB does not contain the raw bulk data but rather “registers” the information about where the server can find this information and some metadata about the object in question. For example, if we have a variant set that is backed by a single VCF file, the registry DB will contain the path to this file as well as the name of the variant set, the reference set it is defined by, and other information necessary to implement the GA4GH protocol. This registry architecture allows us a lot of flexibility in the sources of data that we can use.

Command Line¶

init¶

The init command initialises a new registry DB at a given file path. This is the first command that must be issued when creating a new GA4GH repository.

usage: ga4gh_repo init [-h] [-f] registryPath

Positional arguments:

registryPath

the location of the registry database

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo init registry.db

list¶

The list command is used to print the contents of a repository to the screen. It is an essential tool for administrators to understand the structure of the repository that they are managing.

Note

The list command is under development and will be much more sophisticated in the future. In particular, the output of this command should improve considerably in the near future.

usage: ga4gh_repo list [-h] registryPath

Positional arguments:

registryPath

the location of the registry database

Examples:

$ ga4gh_repo list registry.db

list-announcements¶

To view the announcements the server has received, use this command. It will output the announcements as a TSV that can be imported into a spreadsheet application.

usage: ga4gh_repo list-announcements [-h] registryPath

Positional arguments:

registryPath

the location of the registry database

Examples:

$ ga4gh_repo list-announcements registry.db > announcements.tsv

clear-announcements¶

To clear the received announcements run this command. This cannot be undone.

usage: ga4gh_repo clear-announcements [-h] registryPath

Positional arguments:

registryPath

the location of the registry database

Examples:

$ ga4gh_repo clear-announcements registry.db

verify¶

The verify command is used to check that the integrity of the data in a repository. The command checks each container object in turn and ensures that it can read data from it. Read errors can occur for any number of reasons (for example, a VCF file may have been moved to another location since it was added to the registry), and the verify command allows an administrator to check that all is well in their repository.

Note

The verify command is under development and will be much more sophisticated in the future. In particular, the output of this command should improve considerably in the near future.

usage: ga4gh_repo verify [-h] registryPath

Positional arguments:

registryPath

the location of the registry database

Examples:

$ ga4gh_repo verify registry.db

add-peer¶

The server maintains a list of known peers. To add a peer to this list use the add-peer command.

usage: ga4gh_repo add-peer [-h] [-A ATTRIBUTES] registryPath url

Positional arguments:

`registryPath`	the location of the registry database
`url`	The URL of the given resource

Options:

`-A, --attributes`
	additional attributes for the message expressed as JSON

Examples:

$ ga4gh_repo add-peer http://1kgenomes.ga4gh.org

remove-peer¶

You can remove a peer from the list of peers by its URL.

usage: ga4gh_repo remove-peer [-h] [-f] registryPath url

Positional arguments:

`registryPath`	the location of the registry database
`url`	The URL of the given resource

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-peer http://1kgenomes.ga4gh.org

add-dataset¶

Creates a new dataset in a repository. A dataset is an arbitrary collection of ReadGroupSets, VariantSets, VariantAnnotationSets and FeatureSets. Each dataset has a name, which is used to identify it in the repository manager.

usage: ga4gh_repo add-dataset [-h] [-A ATTRIBUTES] [-d DESCRIPTION]
                              registryPath datasetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset

Options:

`-A, --attributes`
	additional attributes for the message expressed as JSON
`-d, --description`
	The human-readable description of the dataset.

Examples:

$ ga4gh_repo add-dataset registry.db 1kg -d 'Example dataset using 1000 genomes data'

Adds the dataset with the name 1kg and description 'Example dataset using 1000 genomes data' to the registry database registry.db.

add-referenceset¶

Adds a reference set derived from a FASTA file to a repository. Each record in the FASTA file will correspond to a Reference in the new ReferenceSet. The input FASTA file must be compressed with bgzip and indexed using samtools faidx. Each ReferenceSet contains a number of metadata values (.e.g. species) which can be set using command line options.

usage: ga4gh_repo add-referenceset [-h] [-A ATTRIBUTES] [-r] [-n NAME]
                                   [-d DESCRIPTION] [--species SPECIES]
                                   [--isDerived ISDERIVED]
                                   [--assemblyId ASSEMBLYID]
                                   [--sourceAccessions SOURCEACCESSIONS]
                                   [--sourceUri SOURCEURI]
                                   registryPath filePath

Positional arguments:

`registryPath`	the location of the registry database
`filePath`	The path of the FASTA file to use as a reference set. This file must be bgzipped and indexed.

Options:

`-A, --attributes`
	additional attributes for the message expressed as JSON
`-r, --relativePath`
	store relative path in database
`-n, --name`	The name of the reference set
`-d, --description`
	The human-readable description of the reference set.
`--species`	The species ontology term as a JSON string
`--isDerived`	Indicates if this reference set is derived from another
`--assemblyId`	The assembly id
`--sourceAccessions`
	The source accessions (pass as comma-separated list)
`--sourceUri`	The source URI

Examples:

$ ga4gh_repo add-referenceset registry.db hs37d5.fa.gz \
    --description "NCBI37 assembly of the human genome" \
    --species '{"termId": "NCBI:9606", "term": "Homo sapiens"}' \
    --name NCBI37 \
    --sourceUri ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

Adds a reference set used in the 1000 Genomes project using the name NCBI37, also setting the species to 9606 (human).

add-biosample¶

Adds a new biosample to the repository. The biosample argument is a JSON document according to the GA4GH JSON schema.

usage: ga4gh_repo add-biosample [-h]
                                registryPath datasetName biosampleName
                                biosample

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`biosampleName`	the name of the biosample
`biosample`	the JSON of the biosample

Examples:

$ ga4gh_repo add-biosample registry.db dataset1 HG00096 '{"individualId": "abc"}'

Adds the biosample named HG00096 to the repository with the individual ID “abc”.

add-individual¶

Adds a new individual to the repository. The individual argument is a JSON document following the GA4GH JSON schema.

usage: ga4gh_repo add-individual [-h]
                                 registryPath datasetName individualName
                                 individual

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`individualName`	the name of the individual
`individual`	the JSON of the individual

Examples:

$ ga4gh_repo add-individual registry.db dataset1 HG00096 '{"description": "A description"}'

add-ontology¶

Adds a new ontology to the repository. The ontology supplied must be a text file in OBO format. If you wish to serve sequence or variant annotations from a repository, a sequence ontology (SO) instance is required to translate ontology term names held in annotations to ontology IDs. Sequence ontology definitions can be downloaded from the Sequence Ontology site.

usage: ga4gh_repo add-ontology [-h] [-r] [-n NAME] registryPath filePath

Positional arguments:

`registryPath`	the location of the registry database
`filePath`	The path of the OBO file defining this ontology.

Options:

`-r, --relativePath`
	store relative path in database
`-n, --name`	The name of the ontology

Examples:

$ ga4gh_repo add-ontology registry.db path/to/so-xp.obo

Adds the sequence ontology so-xp.obo to the repository using the default naming rules.

add-variantset¶

Adds a variant set to a named dataset in a repository. Variant sets are currently derived from one or more non-overlapping VCF/BCF files which may be either stored locally or come from a remote URL. Multiple VCF files can be specified either directly on the command line or by providing a single directory argument that contains indexed VCF files. If remote URLs are used then index files in the local file system must be provided using the -I option.

usage: ga4gh_repo add-variantset [-h] [-r] [-I indexFiles [indexFiles ...]]
                                 [-n NAME] [-R REFERENCESETNAME]
                                 [-O ONTOLOGYNAME] [-A ATTRIBUTES] [-a]
                                 registryPath datasetName dataFiles
                                 [dataFiles ...]

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`dataFiles`	The VCF/BCF files representing the new VariantSet. These may be specified either one or more paths to local files or remote URLS, or as a path to a local directory containing VCF files. Either a single directory argument may be passed or a list of file paths/URLS, but not a mixture of directories and paths.

Options:

`-r, --relativePath`
	store relative path in database
`-I, --indexFiles`
	The index files for the VCF/BCF files provided in the dataFiles argument. These must be provided in the same order as the data files.
`-n, --name`	The name of the VariantSet
`-R, --referenceSetName`
	the name of the reference set to associate with this VariantSet
`-O, --ontologyName`
	the name of the sequence ontology instance used to translate ontology term names to IDs in this VariantSet
`-A, --attributes`
	additional attributes for the message expressed as JSON
`-a, --addAnnotationSets`
	If the supplied VCF file contains annotations, create the corresponding VariantAnnotationSet.

Examples:

$ ga4gh_repo add-variantset registry.db 1kg 1kgPhase1/ -R NCBI37

Adds a new variant set to the dataset named 1kg in the repository defined by the registry database registry.db using the VCF files contained in the directory 1kgPhase1. Note that this directory must also contain the corresponding indexes for these files. We associate the reference set named NCBI37 with this new variant set. Because we do not provide a --name argument, a name is automatically generated using the default name generation rules.

$ ga4gh_repo add-variantset registry.db 1kg \
    1kgPhase1/chr1.vcf.gz 1kg/chr2.vcf.gz -n phase1-subset -R NCBI37

Like the last example, we add a new variant set to the dataset 1kg, but here we only use the VCFs for chromosomes 1 and 2. We also specify the name for this new variant set to be phase1-subset.

$ ga4gh_repo add-variantset registry.db 1kg \
    --name phase1-subset-remote -R NCBI37 \
    --indexFiles ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi ALL.chr2.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi \
    ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \
    ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ALL.chr2.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz

This example performs the same task of creating a subset of the phase1 VCFs, but this time we use the remote URL directly and do not keep a local copy of the VCF file. Because we are using remote URLs to define the variant set, we have to download a local copy of the corresponding index files and provide them on the command line using the --indexFiles option.

add-readgroupset¶

Adds a readgroup set to a named dataset in a repository. Readgroup sets are currently derived from a single indexed BAM file, which can be either stored locally or based on a remote URL. If the readgroup set is based on a remote URL, then the index file must be stored locally and specified using the --indexFile option.

Each readgroup set must be associated with the reference set that it is aligned to. The add-readgroupset command first examines the headers of the BAM file to see if it contains information about references, and then looks for a reference set with name equal to the genome assembly identifer defined in the header. (Specifically, we read the @SQ header line and use the value of the AS tag as the default reference set name.) If this reference set exists, then the readgroup set will be associated with it automatically. If it does not (or we cannot find the appropriate information in the header), then the add-readgroupset command will fail. In this case, the user must provide the name of the reference set using the --referenceSetName option.

usage: ga4gh_repo add-readgroupset [-h] [-n NAME] [-R REFERENCESETNAME]
                                   [-A ATTRIBUTES] [-r] [-I INDEXFILE]
                                   registryPath datasetName dataFile

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`dataFile`	The file path or URL of the BAM file for this ReadGroupSet

Options:

`-n, --name`	The name of the ReadGroupSet
`-R, --referenceSetName`
	the name of the reference set to associate with this ReadGroupSet
`-A, --attributes`
	additional attributes for the message expressed as JSON
`-r, --relativePath`
	store relative path in database
`-I, --indexFile`
	The file path of the BAM index for this ReadGroupSet. If the dataFile argument is a local file, this will be automatically inferred by appending ‘.bai’ to the file name. If the dataFile is a remote URL the path to a local file containing the BAM index must be provided

Examples:

$ ga4gh_repo add-readgroupset registry.db 1kg \
    path/to/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam

Adds a new readgroup set for an indexed 1000 Genomes BAM file stored on the local file system. The index file follows the usual convention and is stored in the same directory as the BAM file and has an extra .bai extension. The name of the readgroup set is automatically derived from the file name, and the reference set automatically set from the BAM header.

$ ga4gh_repo add-readgroupset registry.db 1kg ga4gh-example-data/HG00096.bam \
    -R GRCh37-subset -n HG0096-subset

Adds a new readgroup set based on a subset of the 1000 genomes reads for the HG00096 sample from the example data used in the reference server. In this case we specify that the reference set name GRCh37-subset be associated with the readgroup set. We also override the default name generation rules and specify the name HG00096-subset for the new readgroup set.

$ ga4gh_repo add-readgroupset registry.db 1kg \
    -n HG00114-remote
    -I /path/to/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai
    ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/HG00114/alignment/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam

Adds a new readgroups set based on a 1000 genomes BAM directly from the NCBI FTP server. Because this readgroup set uses a remote FTP URL, we must specify the location of the .bai index file on the local file system.

add-featureset¶

Adds a feature set to a named dataset in a repository. Feature sets must be in a ‘.db’ file. An appropriate ‘.db’ file can be generate from a GFF3 file using scripts/generate_gff3_db.py.

usage: ga4gh_repo add-featureset [-h] [-A ATTRIBUTES] [-r]
                                 [-R REFERENCESETNAME] [-O ONTOLOGYNAME]
                                 [-C CLASSNAME]
                                 registryPath datasetName filePath

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`filePath`	The path to the converted SQLite database containing Feature data

Options:

`-A, --attributes`
	additional attributes for the message expressed as JSON
`-r, --relativePath`
	store relative path in database
`-R, --referenceSetName`
	the name of the reference set to associate with this feature set
`-O, --ontologyName`
	the name of the sequence ontology instance used to translate ontology term names to IDs in this feature set
`-C, --className`
	the name of the class used to fetch features in this feature set

Examples:

$ ga4gh_repo add-featureset registry.db 1KG gencode.db \
    -R hg37 -O so-xp-simple

Adds the feature set gencode to the registry under the 1KG dataset. The flags set the reference genome to be hg37 and the ontology to use to so-xp-simple.

add-continuousset¶

Adds a continuous set to a named dataset in a repository. Continuous sets must be in a bigWig file. The bigWig format is described here: http://genome.ucsc.edu/goldenPath/help/bigWig.html. There are directions for converting wiggle files to bigWig files on the page also. Files in the bedGraph format can be converted using bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/).

usage: ga4gh_repo add-continuousset [-h] [-r] [-R REFERENCESETNAME]
                                    [-C CLASSNAME]
                                    registryPath datasetName filePath

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`filePath`	The path to the file contianing the continuous data

Options:

`-r, --relativePath`
	store relative path in database
`-R, --referenceSetName`
	the name of the reference set to associate with this continuous set
`-C, --className`
	the name of the class used to fetch features in this continuous set

Examples:

$ ga4gh_repo add-continuousset registry.db 1KG continuous.bw \
    -R hg37

Adds the continuous set continuous to the registry under the 1KG dataset. The flags set the reference genome to be hg37.

init-rnaquantificationset¶

Initializes a rnaquantification set.

usage: ga4gh_repo init-rnaquantificationset [-h] registryPath filePath

Positional arguments:

`registryPath`	the location of the registry database
`filePath`	The path to the resulting Quantification Set

Examples:

$ ga4gh_repo init-rnaquantificationset repo.db rnaseq.db

Initializes the RNA Quantification Set with the filename rnaseq.db.

add-rnaquantification¶

Adds a rnaquantification to a RNA quantification set.

RNA quantification formats supported are currently kallisto and RSEM.

usage: ga4gh_repo add-rnaquantification [-h] [--biosampleName BIOSAMPLENAME]
                                        [--readGroupSetName READGROUPSETNAME]
                                        [--featureSetNames FEATURESETNAMES]
                                        [-n NAME] [-d DESCRIPTION] [-t]
                                        [-A ATTRIBUTES]
                                        filePath quantificationFilePath format
                                        registryPath datasetName

Positional arguments:

`filePath`	The path to the RNA SQLite database to create or modify
`quantificationFilePath`
	The path to the expression file.
`format`	format of the quantification input data
`registryPath`	the location of the registry database
`datasetName`	the name of the dataset

Options:

`--biosampleName`
	Biosample Name
`--readGroupSetName`
	Read Group Set Name
`--featureSetNames`
	Comma separated list
`-n, --name`	The name of the rna quantification
`-d, --description`
	The human-readable description of the RnaQuantification.
`-t, --transcript`
	sets the quantification type to transcript
`-A, --attributes`
	additional attributes for the message expressed as JSON

Examples:

$ ga4gh_repo add-rnaquantification rnaseq.db data.tsv \
         kallisto ga4gh-example-data/registry.db brca1 \
        --biosampleName HG00096 --featureSetNames gencodev19
        --readGroupSetName HG00096rna --transcript

Adds the data.tsv in kallisto format to the rnaseq.db quantification set with optional fields for associating a quantification with a Feature Set, Read Group Set, and Biosample.

add-rnaquantificationset¶

When the desired RNA quantification have been added to the set, use this command to add them to the registry.

usage: ga4gh_repo add-rnaquantificationset [-h] [-R REFERENCESETNAME]
                                           [-n NAME] [-A ATTRIBUTES]
                                           registryPath datasetName filePath

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`filePath`	The path to the converted SQLite database containing RNA data

Options:

`-R, --referenceSetName`
	the name of the reference set to associate with this RnaQuantificationSet
`-n, --name`	The name of the RnaQuantificationSet
`-A, --attributes`
	additional attributes for the message expressed as JSON

Examples:

$ ga4gh_repo add-rnaquantificationset registry.db brca1 rnaseq.db \
    -R hg37 -n rnaseq

Adds the RNA quantification set rnaseq.db to the registry under the brca1 dataset. The flags set the reference genome to be hg37 and the name of the set to rnaseq.

add-phenotypeassociationset¶

Adds an rdf object store. The cancer genome database Clinical Genomics Knowledge Base http://nif-crawler.neuinfo.org/monarch/ttl/cgd.ttl, published by the Monarch project, is the supported format for Evidence.

usage: ga4gh_repo add-phenotypeassociationset [-h] [-n NAME] [-A ATTRIBUTES]
                                              registryPath datasetName dirPath

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`dirPath`	The path of the directory containing ttl files.

Options:

`-n, --name`	The name of the PhenotypeAssociationSet
`-A, --attributes`
	additional attributes for the message expressed as JSON

Examples:

$ ga4gh_repo add-phenotypeassociationset registry.db dataset1 /monarch/ttl/cgd.ttl -n cgd

remove-dataset¶

Removes a dataset from the repository and recursively removes all objects (ReadGroupSets, VariantSets, etc) within this dataset.

usage: ga4gh_repo remove-dataset [-h] [-f] registryPath datasetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-dataset registry.db dataset1

Deletes the dataset with name dataset1 from the repository represented by registry.db

remove-referenceset¶

Removes a reference set from the repository. Attempting to remove a reference set that is referenced by other objects in the repository will result in an error.

usage: ga4gh_repo remove-referenceset [-h] [-f] registryPath referenceSetName

Positional arguments:

`registryPath`	the location of the registry database
`referenceSetName`
	the name of the reference set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-referenceset registry.db NCBI37

Deletes the reference set with name NCBI37 from the repository represented by registry.db

remove-biosample¶

Removes a biosample from the repository.

usage: ga4gh_repo remove-biosample [-h] [-f]
                                   registryPath datasetName biosampleName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`biosampleName`	the name of the biosample

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-biosample registry.db dataset1 HG00096

Deletes the biosample with name HG00096 in the dataset dataset1 from the repository represented by registry.db

remove-individual¶

Removes an individual from the repository.

usage: ga4gh_repo remove-individual [-h] [-f]
                                    registryPath datasetName individualName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`individualName`	the name of the individual

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-individual registry.db dataset1 HG00096

Deletes the individual with name HG00096 in the dataset dataset1 from the repository represented by registry.db

remove-ontology¶

Removes an ontology from the repository. Attempting to remove an ontology that is referenced by other objects in the repository will result in an error.

usage: ga4gh_repo remove-ontology [-h] [-f] registryPath ontologyName

Positional arguments:

`registryPath`	the location of the registry database
`ontologyName`	the name of the ontology

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-ontology registry.db so-xp

Deletes the ontology with name so-xp from the repository represented by registry.db

remove-variantset¶

Removes a variant set from the repository. This also deletes all associated call sets and variant annotation sets from the repository.

usage: ga4gh_repo remove-variantset [-h] [-f]
                                    registryPath datasetName variantSetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`variantSetName`	the name of the variant set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-variantset registry.db dataset1 phase3-release

Deletes the variant set named phase3-release from the dataset named dataset1 from the repository represented by registry.db.

remove-readgroupset¶

Removes a read group set from the repository.

usage: ga4gh_repo remove-readgroupset [-h] [-f]
                                      registryPath datasetName
                                      readGroupSetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`readGroupSetName`
	the name of the read group set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-readgroupset registry.db dataset1 HG00114

Deletes the readgroup set named HG00114 from the dataset named dataset1 from the repository represented by registry.db.

remove-featureset¶

Removes a feature set from the repository.

usage: ga4gh_repo remove-featureset [-h] [-f]
                                    registryPath datasetName featureSetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`featureSetName`	the name of the feature set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-featureset registry.db 1KG gencode-genes

Deletes the feature set named gencode-genes from the dataset named 1KG from the repository represented by registry.db.

remove-continuousset¶

Removes a continuous set from the repository.

usage: ga4gh_repo remove-continuousset [-h] [-f]
                                       registryPath datasetName
                                       continuousSetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`continuousSetName`
	the name of the continuous set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-continuousset registry.db 1KG continuous

Deletes the feature set named continuous from the dataset named 1KG from the repository represented by registry.db.

remove-rnaquantificationset¶

Removes a rna quantification set from the repository.

usage: ga4gh_repo remove-rnaquantificationset [-h] [-f]
                                              registryPath datasetName
                                              rnaQuantificationSetName

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`rnaQuantificationSetName`
	the name of the RNA Quantification Set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-rnaquantificationset registry.db dataset1 ENCFF305LZB

Deletes the rnaquantification set named ENCFF305LZB from the dataset named dataset1 from the repository represented by registry.db.

remove-phenotypeassociationset¶

Removes an rdf object store.

usage: ga4gh_repo remove-phenotypeassociationset [-h] [-f]
                                                 registryPath datasetName name

Positional arguments:

`registryPath`	the location of the registry database
`datasetName`	the name of the dataset
`name`	The name of the phenotype association set

Options:

-f, --force

do not prompt for confirmation

Examples:

$ ga4gh_repo remove-phenotypeassociationset registry.db dataset1  cgd