Skip to main content

A standard variation file format for human genome sequences

Abstract

Here we describe the Genome Variation Format (GVF) and the 10Gen dataset. GVF, an extension of Generic Feature Format version 3 (GFF3), is a simple tab-delimited format for DNA variant files, which uses Sequence Ontology to describe genome variation data. The 10Gen dataset, ten human genomes in GVF format, is freely available for community analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon's EC2 cloud computing environment.

Background

With the advent of personalized genomics we have seen the first examples of fully sequenced individuals [1–9]. Now, next generation sequencing technologies promise to radically increase the number of human sequences in the public domain. These data will come not just from large sequencing centers, but also from individual laboratories. For reasons of resource economy, 'variant files' rather than raw sequence reads or assembled genomes are rapidly emerging as the common currency for exchange and analysis of next generation whole genome re-sequencing data. Several data formats have emerged recently for sequencing reads (SRF) [10], read alignments (SAM/BAM) [11], genotype likelihoods/posterior SNP probabilities (GLF) [12], and variant calling (VCF) [13]. However, the resulting variant files of single nucleotide variants (SNVs) and structural variants (SVs) are still distributed as non-standardized tabular text files, with each sequence provider producing its own idiomatic data files [1–9]. The lack of a standard format complicates comparisons of data from multiple sources and across projects and sequencing platforms, tremendously slowing the progress of comparative personal genome analysis. In response we have developed GVF, the Genome Variation Format.

GVF [14] is an extension of the widely used Generic Feature Format version 3 (GFF3) standard for describing genome annotation data. The GFF3 format [15] was developed to permit the exchange and comparison of gene annotations between different model organism databases [16]. GFF3 is based on the General Feature Format (GFF), which was originally developed during the human genome project to compare human genome annotations [17]. Importantly, GFF3, unlike GFF, is typed using an ontology. This means that the terminology being used to describe the data is standardized, and organized by pre-specified relationships. The attribute specification structure of GFF3 files allows extensibility in specifying feature-specific data for different types of features and it is this extensibility that GVF capitalizes on in defining sequence alteration specific data types. Annotation databases have historically developed different in-house schemas; thus, such standardization is required to ensure interoperability between databases and for comparative analyses.

While there are richer ways of representing genomic features using XML (Extensible Markup Language) and relational database schemas, simple text-based, tab-delimited files have persisted in bioinformatics because they balance human with computer readability. Since its adoption as the basic exchange format, two aspects of GFF3 have emerged as essential for success. First, it must be simple for software to produce and parse; second, its contents need to be typed using terms drawn from an ontology. The first aspect means that humans can easily read and edit files with a text editor and perform simple analyses with command-line software tools. The second aspect not only constrains different database curators to use the same terminologies, but also, because of the formal structure of the ontology, allows automated reasoning on the contents of such a file. It therefore prevents ambiguities and conflicting terminologies. GVF builds upon these strengths of GFF3, adopting GFF3's simple, tab-delimited format; and like GFF3, the contents of GVF files are described using the Sequence Ontology (SO) - an ontology developed by the Gene Ontology Consortium [18] to describe the parts of genomic annotations, and how these parts relate to each other [19, 20]. Using SO to type both the features and the consequences of a variation gives GVF files the flexibility necessary to capture a wide variety of variation data, while still maintaining unified semantics and a simple file format. For example, GVF files can contain both re-sequencing and DNA genotyping microarray experiment data. In addition, GVF capitalizes on the extensibility of GFF3 to specify a rich set of attributes specific to sequence alterations in a structured way. An added benefit of GVF's compliance with GFF3 is that existing parsers, visualization and validation software, such as those developed by the Generic Model Organism Database (GMOD) project to operate on GFF3 files can be used to manipulate and view GVF files. Thus, the GVF complements existing gene and variant nomenclature efforts [21], and provides a simple ontology-based sequence-centric genome file format linking variants to genome positions and genome annotations.

Below we describe the GVF standard and the various additions we have made to GFF3 and SO to support it. We also briefly describe the conversion of the first ten publicly available personal genomes into GVF format. These GVF files are available for download and for cloud computation. We will refer to these data as the 10Gen dataset. This is provided as a service to the biomedical community as a reference dataset for whole genome comparative analyses and software development. This dataset will hopefully foster the development of new tools for the analyses of personal genome sequences.

Results

We have extended both the GFF3 specification and SO to allow the rigorous description of sequence variations with respect to a reference genome. The first eight columns of a GFF3 file specify the type and source of a feature, its location on a reference sequence, and optionally a score, strand and phase. These columns of data are incorporated into GVF unchanged. The GFF3 format additionally provides the option to append attributes to a sequence feature using tag-value pairs in the ninth column and it is here that GVF specifies additional structure to annotate sequence alteration specific data (Table 1). Effectively describing sequence variants in this fashion has three prerequisites. First, a standard vocabulary is required for additional tags and values. Second, the vocabulary must be defined in a machine-readable fashion. And finally - in order to facilitate downstream analyses - the relationships between terms used must be formally specified using an ontology. In addition to SO, GVF also allows, but does not require, the use of other ontologies such as the PATO, an ontology of phenotypic qualities [22] and the Human Phenotype Ontology (HPO) [23] to categorize the phenotype of the individual.

Table 1 A summary of the tag-value pairs, and their requirement for GVF

The SO has been extended in order to describe both the nature of the observed variants and the effects that the variants might have. SO is part of the Open Biological and Biomedical Ontologies (OBO) Library [24], and follows the recommendations and formalisms of the OBO Foundry [25]. This enables machine reasoning across GVF data files using the rich collection of software tools and libraries developed for use with OBO. The key top-level terms are shown in Figure 1. The logic and structure imposed by an upper level ontology means that existing and novel feature annotations are easily added and then immediately computable.

Figure 1
figure 1

The top-level terms in the Sequence Ontology used in variant annotation. There are 1,792 terms in SO, most of which (1,312) are sequence features. There are 100 terms in the ontology that are kinds of sequence variant, of which the two top level terms are shown, and three sub-types, shown with dashed lines, that demonstrate the detail of these terms. The parts of SO that are used to annotate sequence variation files are sequence alteration to categorize the change (five subtypes shown with dashed lines), sequence feature to annotate the genomic features that the alteration intersects, and sequence variant to annotate the kind of sequence variant with regards to the reference sequence.

GVF: a specification for genome variant description

Figure 2 shows several lines from a typical GVF file. As in GFF3, there are three types of lines: those beginning with '##' specify file-wide pragmas - global features of the genome as a whole; lines beginning with '#' are unstructured comments; and all remaining lines described features of the sequence.

Figure 2
figure 2

An example of a GVF annotation, showing three hypothetical sequence alterations: an SNV, a deletion and a duplication. Lines beginning with '##' specify file-wide pragmas that apply to all or a large portion of the file. Lines are broken over multiple lines and separated by empty lines for presentation in the manuscript, but all data for a given pragma or feature should be contained on one line in a GVF file. A description of the tag-value pairs is given in Table 1.

GVF provides nine new pragmas to describe the reference sequence and the methods used to call variants. These pragmas are described in detail in Table 2. The existing genome-build pragma of GFF is mandatory, as all GVF files are dependent on a reference sequence to specify variant positions. While most of the examples discussed here are human genome sequence variants, GVF is a truly generic format. A GVF file can contain sequence variants identified in other organisms as well as identified by DNA microarrays (see example on 10Gen web site for NA_19240). GVF files can also contain variants identified in collections of individuals, as well as population data. The GFF3 species pragma is used to specify other organisms. If one wants to specify multiple individuals in the same file, it is denoted using the source field, and the population_freq tag is provided to describe the frequency of a variant within a population (for example, see the Ensembl database distribution in GVF).

Table 2 The pragmas defined by GVF, in addition to those already defined by GFF3 (gff-version, sequence-region, feature-ontology, attribute-ontology, source-ontology, species, genome-build)

Each of the rows in a GVF file describes a single variant from an individual or population. Each such variant is typed using the SO terms that can describe SNVs, any size of nucleotide insertion or deletion, copy number variations, large structural variations or any of the 38 terms currently related to sequence alterations in SO. In the case of a seemingly complex variation, such as an SNV located within a translocation, each sequence alteration is annotated relative to its location on the reference genome, on a separate line in the file.

The most flexible part of a feature description in GFF3 is the ninth column, where attributes of a feature are given as tag-value pairs (Table 1). It is here that GVF provides additional structure specific to sequence alteration features. Like GFF3, the attribute tag-value pairs in GVF can come in any order. Multiple tag-value pairs are separated from each other by semicolons, tags are separated from values by '=', and multiple values are comma delimited. GVF includes the tags specified by the GFF3 specification, such as ID, Name, Alias, and so on, and in addition 11 additional tags that allow for the annotation of sequence alteration features and constrains the values for some of those attributes to portions of the SO. For example, the sequence of the variant as well as the reference sequence at that position are specified by Variant_seq and Reference_seq tags, respectively. In the case of sequence-based variant calling methods, the number of reads supporting the variant can be given by the Variant_reads tag. The genotype at the variant locus is specified with the Genotype tag. Other features annotated on the genome (gene, mRNA, exon, splice site, transcription start site, and so on) that intersect the variant, along with the effect that the variant has on the feature, are annotated with the Variant_effect tag. For variant sequences that involve deletion or duplication of large regions of the reference sequence, the copy number of the region may be given with the Variant_copy_number tag. Table 1 provides the details for the tags discussed here and the allowed values.

While a great deal of personal genome variation data today comes from next generation sequencing technologies, the GVF standard can also be used to describe variant data from any source creating DNA variation data with nucleotide resolution, including genotyping DNA microarrays, comparative genomic hybridization (CGH) arrays, and others.

Because GVF is a fully compliant extension of GFF3, GVF files provide a basis for exploration and analysis of personal genome sequences with the widely used Bioperl [26], and GMOD toolkits [27]; variant annotations can be viewed by browsers such as GBrowse [28], JBrowse [29], Apollo [30], and analyzed, for example, using the Comparative Genomics Library (CGL) [31]. This means that a GVF file can be passed through a series of analyses, each step adding various attributes to the file, allowing a GVF file to grow progressively richer with each analysis. Complete documentation is available from the website [14].

A reference personal genomes dataset - '10Gen'

Gold standards and reference datasets are invaluable for software development, testing and for benchmarking the performance of algorithms and tool sets. Classic examples in genomics include the CASP (Competitive Assessment of Protein fold recognition) workshop and its datasets for protein structure comparisons [32, 33], the GASP (Genome Annotation Assessment in Drosophila melanogaster) [34], EGASP (ENCODE Genome Annotation Assessment Project) [35, 36], and NGASP (Nematode Genome Annotation Assessment Project) [37] datasets for gene finding and genome annotation, and the Eisen et al. [38] gene expression dataset for microarray analyses. As proof-of-principle for the GVF standard and to facilitate personal genome analyses and the development of software for such analyses, we have parsed the original variant files for ten publicly available personal genome sequences and assembled their variant information in GVF format (Table 3). These ten genomes come from diverse ethnic backgrounds and were produced using a variety of sequencing platforms. Also included in the dataset is a single genome (NA_18507) sequenced with two different technologies. For the genome NA_19240 we present the published DNA genotype microarray data (HumanHap550) variants in gvf format as an additional file. These features of the GVF dataset mean that it is an ideal test dataset for a wide array of anthropological analyses, technical comparisons of sequencing platforms, and eventually personal health analyses. The source data for each GVF file is given in the methods section.

Table 3 A reference GVF dataset for public use

Discussion

To fulfill the promise of personal whole genome sequencing it will be critical to compare individual genomes to the reference genome and to one another. One lesson learned from comparative genomics analyses [31–34, 37] is that accurate and easy comparisons require a standardized data format. Without a data standard, ambiguities and misunderstandings poison comparative analyses. The GFF3 standard has been widely embraced by the model organism community as a solution to these problems. GVF will provide the same benefits for personal genomics. Although some of the variant file formats currently in use [1–8] and VCF [13] are GFF3-like in spirit, none is a formal extension of GFF3, meaning that their terminologies (tags) are not formally defined, versioned, maintained or OBO compliant [25]. GVF also differs from existing formats in matters of scope. First, GVF is not limited to re-sequencing applications; it also can be used to describe DNA genotyping chip experiments, re-sequencing and DNA-chip data can even be combined in a single file. Second, GVF provides more than just a means to describe how and why a variant was called; it provides an extensive terminology with which to describe a variant's relationship to - and impact upon - other features annotated on a genome.

Rigorously grounding GVF upon the GFF3 specification has many other benefits as well. Because both file formats are typed using the SO, GFF3 and GVF files can be used together in a synergistic fashion. Moreover, because GVF is a formal extension of the GFF3 standard, existing parsers, visualization tools and validation software, such as those developed by the GMOD project [16] to operate on GFF3 files, can used to manipulate and view GVF files. This will provide enormous benefits for those seeking to analyze personal human genomics data.

In order to jumpstart such analyses, we have also manufactured a reference dataset of variants from ten personal genomes, the 10Gen dataset. These genomes represent a diverse assortment of ethnicities, and were produced using a variety of sequencing platforms. Our hope is that the 10Gen dataset will be used as a benchmark for personal genomics software development, following in the footsteps of other successful benchmark datasets, such as those used by CASP [32, 33] for protein structures, GASP/EGASP/NGASP [34, 35, 37] for gene structures, and Eisen/MIAME (Minimum Information about a Microarray Experiment) [38–40] for gene expression, to name just a few. Moreover, the simplicity of the GVF file format combined with the rigor of its formal specification make GVF ideal for adoption by technology providers, genome centers, population geneticists, computational biologists, evolutionary biologists, health care providers, and clinical testing laboratories.

Materials and methods

Extensions to the Sequence Ontology

Using OBO-Edit [41] the SO was extended in three areas: sequence_alteration, sequence_feature and sequence_variant. There are 38 terms to represent the kinds of sequence alteration, 1,283 terms to represent features intersected by the alteration and 100 terms to represent the variant caused by a sequence alteration, such as intergenic_variant and non_synonymous_codon (see the MISO Sequence Ontology Browser on the SO website [42] for complete details).

Variant files for ten genomes

The variant files from the ten genomes were downloaded from web sites indicated in the references listed in Table 3. These files were converted to GVF format and were manually spot checked for consistency with annotations on the UCSC Genome Browser. They were then analyzed with a genome variation software pipeline that provided additional quality and consistency checks with respect to the NCBI build 36 of the human genome assembly and with data in the dbSNP and OMIM (Online Mendelian Inheritance in Man) databases.

The GVF standard can also be used to describe genotyping DNA microarray-based variant calls. This flexibility means that a single parser can process variant files from both sequencing and DNA genotyping microarray experiments; moreover, because these fields are attributes of the variant, not the file, a single GVF file can contain variants from heterogeneous sets of sequencing and microarray platforms.

Data downloads

The 10Gen dataset is available for download [43]. Each variant file is named as denoted in Table 3 and additional details are documented in a README file within the download directory. In addition, a cloud compatible version of the data is available as an Amazon elastic block storage (EBS) snapshot [44]. Details for using the snapshot are available from the 10Gen website [43]. This set provides a standard reference dataset and a means to benchmark new analysis procedures. GVF files are also available for download of variant data from Ensembl.

Abbreviations

CASP:

Competitive Assessment of Protein fold recognition

EGASP:

ENCODE Genome Annotation Assessment Project

GASP:

Genome Annotation Assessment in Drosophila melanogaster

GFF:

General Feature Format

GFF3:

Generic Feature Format version 3

GMOD:

Generic Model Organism Database

GVF:

Genome Variation Format

NCBI:

National Center for Biotechnology Information

NGASP:

Nematode Genome Annotation Assessment Project

OBO:

Open Biological and Biomedical Ontologies

SNP:

single nucleotide polymorphism

SNV:

single nucleotide variation

SO:

Sequence Ontology

VCF:

Variant Call Format.

References

  1. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, et al: The diploid genome sequence of an individual human. PLoS Biol. 2007, 5: e254-10.1371/journal.pbio.0050254.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM: The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008, 452: 872-876. 10.1038/nature06884.

    Article  PubMed  CAS  Google Scholar 

  3. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, et al: Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009, 19: 1527-1541. 10.1101/gr.091868.109.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  4. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456: 53-59. 10.1038/nature07517.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  5. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, et al: The diploid genome sequence of an Asian individual. Nature. 2008, 456: 60-65. 10.1038/nature07484.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ: The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res. 2009, 19: 1622-1629. 10.1101/gr.092197.109.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  7. Pushkarev D, Neff NF, Quake SR: Single-molecule sequencing of an individual human genome. Nat Biotechnol. 2009, 27: 847-852. 10.1038/nbt.1561.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, et al: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010, 327: 78-81. 10.1126/science.1181498.

    Article  PubMed  CAS  Google Scholar 

  9. 1000 Genomes Project. [http://www.1000genomes.org]

  10. Sequence Read Format. [http://srf.sourceforge.net]

  11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25: 2078-2079. 10.1093/bioinformatics/btp352.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Genotype Likelihood Format. [http://maq.sourceforge.net/glfProgs.shtml]

  13. Variant Call Format. [http://vcftools.sourceforge.net]

  14. Genome Variation Format. [http://www.sequenceontology.org/gvf.html]

  15. Generic Feature Format version 3. [http://www.sequenceontology.org/resources/gff3.html]

  16. Generic Model Organism Database. [http://www.gmod.org]

  17. GFF. [http://www.sanger.ac.uk/resources/software/gff/spec.html]

  18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  19. Eilbeck K, Lewis SE: Sequence ontology annotation guide. Comp Funct Genomics. 2004, 5: 642-647. 10.1002/cfg.446.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  20. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M: The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005, 6: R44-10.1186/gb-2005-6-5-r44.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Oetting WS: Clinical genetics and human genome variation: the 2008 Human Genome Variation Society scientific meeting. Hum Mutat. 2009, 30: 852-856. 10.1002/humu.20987.

    Article  PubMed  Google Scholar 

  22. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M: The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2008, 36: D768-772. 10.1093/nar/gkm956.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  23. Robinson PN, Mundlos S: The human phenotype ontology. Clin Genet. 2010, 77: 525-534. 10.1111/j.1399-0004.2010.01436.x.

    Article  PubMed  CAS  Google Scholar 

  24. The Open Biological and Biomedical Ontologies. [http://www.obofoundry.org/]

  25. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25: 1251-1255. 10.1038/nbt1346.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  26. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The bioperl toolkit: perl modules for the life sciences. Genome Res. 2002, 12: 1611-1618. 10.1101/gr.361602.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  27. O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD: GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol. 2008, 9: R102-10.1186/gb-2008-9-6-r102.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res. 2002, 12: 1599-1610. 10.1101/gr.403602.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  29. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH: JBrowse: a next-generation genome browser. Genome Res. 2009, 19: 1630-1638. 10.1101/gr.094607.109.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  30. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME: Apollo: a sequence annotation editor. Genome Biol. 2002, 3: RESEARCH0082-10.1186/gb-2002-3-12-research0082.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  31. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM: Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2006, 2: e15-10.1371/journal.pcbi.0020015.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Levitt M: Competitive assessment of protein fold recognition and alignment accuracy. Proteins. 1997, Suppl 1: 92-104. 10.1002/(SICI)1097-0134(1997)1+<92::AID-PROT13>3.0.CO;2-M.

    Article  PubMed  CAS  Google Scholar 

  33. Moult J, Hubbard T, Bryant SH, Fidelis K, Pedersen JT: Critical assessment of methods of protein structure prediction (CASP): round II. Proteins. 1997, Suppl 1: 2-6. 10.1002/(SICI)1097-0134(1997)1+<2::AID-PROT2>3.0.CO;2-T.

    Article  PubMed  CAS  Google Scholar 

  34. Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE: Genome annotation assessment in Drosophila melanogaster. Genome Res. 2000, 10: 483-501. 10.1101/gr.10.4.483.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  35. Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006, 7 Suppl 1: S2.1-S2.31. 10.1186/gb-2006-7-s1-s2.

    Google Scholar 

  36. Reese MG, Guigo R: EGASP: Introduction. Genome Biol. 2006, 7 Suppl 1: S1.1-S1.3. 10.1186/gb-2006-7-s1-s1.

    Google Scholar 

  37. Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, Stein LD: nGASP - the nematode genome annotation assessment project. BMC Bioinformatics. 2008, 9: 549-10.1186/1471-2105-9-549.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  39. Brazma A: Minimum Information About a Microarray Experiment (MIAME) - successes, failures, challenges. ScientificWorldJournal. 2009, 9: 420-423. 10.1100/tsw.2009.57.

    Article  PubMed  CAS  Google Scholar 

  40. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet. 2001, 29: 365-371. 10.1038/ng1201-365.

    Article  PubMed  CAS  Google Scholar 

  41. Day-Richter J, Harris MA, Haendel M, Lewis S: OBO-Edit - an ontology editor for biologists. Bioinformatics. 2007, 23: 2198-2200. 10.1093/bioinformatics/btm112.

    Article  PubMed  CAS  Google Scholar 

  42. MISO Sequence Ontology Browser. [http://www.sequenceontology.org/miso]

  43. 10Gen at Sequence Ontology. [http://www.sequenceontology.org/resources/10Gen.html]

  44. 10Gen at Amazon. [http://10gen-gvf.s3.amazonaws.com/list.html]

  45. Database list. [ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs]

  46. Database list details. [ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs_spec]

Download references

Acknowledgements

We thank Francisco De La Vega and Kevin McKernan of Life Technologies for providing early data access. We also acknowledge the 1000 Genomes Project for making data publicly available. This work is supported by NIH/NHGRI grants 5R01HG004341 and P41HG002273 (KE), 1RC2HG005619 (MY and MGR), 2R44HG002991 (MGR) and 2R44HG003667 (MGR and MY).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Martin G Reese or Karen Eilbeck.

Additional information

Authors' contributions

MGR, MY and KE conceived the project. BM, CB, FS, LS, KE developed technical aspects. BM maintains the GVF specification and data repository. All authors contributed intellectually to the development of the project. MGR, MY and KE wrote the manuscript with input from the authors.

Authors’ original submitted files for images

Below are the links to the authors’ original submitted files for images.

Authors’ original file for figure 1

Authors’ original file for figure 2

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reese, M.G., Moore, B., Batchelor, C. et al. A standard variation file format for human genome sequences. Genome Biol 11, R88 (2010). https://doi.org/10.1186/gb-2010-11-8-r88

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/gb-2010-11-8-r88

Keywords