standards > model/format > DOI:10.25504/FAIRsharing.cfzz0h


ready Variant Call Format

Abbreviation:VCF


General Information
Variant Call Format (VCF) is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome.



How to cite this record FAIRsharing.org: VCF; Variant Call Format; DOI: https://doi.org/10.25504/FAIRsharing.cfzz0h; Last edited: Feb. 22, 2018, 2:03 p.m.; Last accessed: Sep 26 2018 10:20 a.m.


Record updated: Aug. 12, 2016, 11:44 a.m. by The FAIRsharing Team.






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Implementing Databases (10)
UCSC Genome Browser database
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.

Ensembl
The Ensembl project is based at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). It provides one of the most comprehensive and integrated resources of genomic data, which can be accessed through the web (www.ensembl.org) and through BioMart, FTP, Perl APIs, REST API and MySQL queries.

SoyBase
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current 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.

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
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 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).

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Grant Number(s)

  • WT104947/Z/14/Z (The Wellcome Trust)