Variant Call Format
Countries that developed this resource United Kingdom
How to cite this record FAIRsharing.org: VCF; Variant Call Format; DOI: https://doi.org/10.25504/FAIRsharing.cfzz0h; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Oct 19 2021 2:09 p.m.
Record updated: Aug. 12, 2016, 11:44 a.m. by The FAIRsharing Team.
|online documentation||http://samtools.github.io/hts-specs/VCFv ...|
|online documentation||http://samtools.github.io/hts-specs/VCFv ...|
No XSD schemas defined
Conditions of Use
No publications available
No guidelines defined
No semantic standards defined
Models and Formats
No syntax standards defined
No identifier schema standards defined
No metrics standards defined
Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.
The European Genome-phenome Archive
The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.
Database of Genotypes and Phenotypes
The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.
Catalogue of Somatic Mutations in Cancer
The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.
Genetic and Genomic Information System
GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible.
RNA Binding Protein Variant Database
RBP-Var is a database of functional variants involved in regulation mediated by RNA-binding proteins. Human genome variants can change the RNA structure and affect RNA-protein interactions.
Dog Genome SNP Database
Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog's population, evolution, phenotype and life habit.
Japanese Genotype-phenotype Archive
The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted.
The Triticeae Toolbox
The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Agriculture (USDA). The current project is funded through NIFA's International Wheat Yield Partnership (IWYP) and part of the Agriculture and Food Research Initiative (AFRI).
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
The International Genome Sample Resource
The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.
Genome Variation Map
The Genome Variation Map (GVM) is a public data repository of genome variations, including single nucleotide polymorphisms (SNP) and small insertions and deletions (INDEL), with particular focuses on human as well as cultivated plants and domesticated animals. GVM collects, integrates and visualizes genome variations for a wide variety of species, accepts submissions of different types of genome variations from all over the world and provides open access for all publicly available data. Based on a large collection of raw sequence data from public repositories, GVM integrates a large number of genome variants for a number of species and provides web interfaces for data submission, search, browse and visualization.
National Cancer Institute's Genomic Data Commons
The National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is a data sharing The National Cancer Institute's Genomic Data Commons (GDC) was created to promote precision medicine in oncology. It supports the import and standardization of genomic and clinical data from cancer research programs. The GDC contains NCI-generated data from some of the largest and most comprehensive cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET). For the first time, these datasets have been harmonized using a common set of bioinformatics pipelines, so that the data can be directly compared. As a growing knowledge system for cancer, the GDC also enables researchers to submit data, and harmonizes these data for import into the GDC.
National Institute of Mental Health Data Archive
The National Institute of Mental Health Data Archive (NDA), originally established to support autism research, is an informatics platform and data repository that facilitates data sharing across all of mental health and other research communities, combining data from each of these repositories into a single resource with a single process for gaining access to all shared data. While querying and browsing data is publicly available, all subject-level data is available behind a login.
Scroll for more...
This record is not implemented by any policy.
This record is in need of a maintainer. If you login, you'll be able to claim this record.
The Wellcome Trust, UK (Charitable foundation)
WT104947/Z/14/Z (The Wellcome Trust, UK)