Skip to content
This repository has been archived by the owner on Jan 24, 2018. It is now read-only.

Latest commit

 

History

History
649 lines (468 loc) · 18.7 KB

datarepo.rst

File metadata and controls

649 lines (468 loc) · 18.7 KB
Raw

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.

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.

Examples:

$ ga4gh_repo list 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.

Examples:

$ ga4gh_repo verify registry.db

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.

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. ncbiTaxonId) which can be set using command line options.

Examples:

$ ga4gh_repo add-referenceset registry.db hs37d5.fa.gz \
    --description "NCBI37 assembly of the human genome" \
    --ncbiTaxonId 9606 --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 ncbiTaxonId 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.

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.

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.

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.

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.

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.

init-rnaquantificationset

Initializes a rnaquantification 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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-rnaquantificationset

Removes a rna quantification set from the repository.

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.

Examples:

$ ga4gh_repo remove-phenotypeassociationset registry.db dataset1  cgd