The VCF specification is no longer maintained by the 1000 Genomes project. The group leading the management and expansion of the format is the Global Alliance for Genomics and Health `GA4GH) large-scale genomics workflow file format team,[7] ga4gh.org/#/fileformats-team However, this flexibility comes at a cost, as downstream processing software may need to account for differences in output formats. At GenomOncology, where we integrate with a variety of DNA sequencers and variant callers, we have invested in creating our highly configurable VCF processing software to quickly adapt to new VCF formats we might encounter. Microsoft Outlook supports opening VCF files as well as converting to a number of other formats such as the popular MSG format. The VCF file format has been extended over time from version 2.1 to 4.0 and detailed information has been added to the file format. The format is also used to export phone contacts and later to import them to another device. Variant Call Format (VCF) is a specification [1] for storing genotype data in a tab-delimited file format. Below is a high-level diagram of a typical bioinformatics pipeline that generates a VCF file: We describe a generic format for storing the most common types of sequence variations. The format is very flexible and can be customized to store a variety of information. It has already been adopted by a number of major projects and is supported by a growing number of software tools. This metasection also declares and describes the fields provided at both the site level (INFO) and the sample level (FORMAT) in the data rows. Here are some examples of each type of VCF specification document: It is strongly recommended that you include lines of information describing the INFO, FILTER, and FORMAT entries used in the body of the VCF file in the meta information section. Although optional, these lines, if present, must be completely well formed.
VCF is flexible and allows you to express virtually any type of variation by listing both the reference haplotype (the REF column) and the alternative haplotypes (the ALT column). This allows for redundancy so that the same event can be expressed in different ways by including a different number of baselines or by combining two adjacent SNPs into a single haplotype (Fig. 1g). Users are advised to follow the recommended practice where possible: a baseline for SNPs and inserts and an alternative baseline for deletions. In cases where the position is ambiguous, the lowest possible coordinate shall be used. When comparing or merging Indel variants, variant haplotypes should be reconstructed and matched, as in the example in Figure 1g, although the exact type of transition may be arbitrary. For larger and more complex variants, citing large sequences becomes impractical and, in these cases, annotations in the INFO column can be used to describe the variant (Fig. 1f). The full VCF specification also includes a number of best practices for describing complex variants. The VCF specification contains several common keywords with a standardized meaning. The following list contains some examples of reserved tags.
VCF is the default file format for storing variation data. It is used by large-scale variant mapping projects such as IGSR. It is also the standard output of variant invocation software such as GATK and the standard input for variant analysis tools such as VEP or for variation archives such as EVA. 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, 2Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, 3Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, 4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, 5Department of Biology, Boston College, MA 02467, 6National Institutes of Health National Center for Biotechnology Information, MD 20894, USA and 7Department of Statistics, University of Oxford, Oxford OX1 3TG, UK If genotype information is available, the same types of data should be present for all samples. First, a FORMAT field is specified that specifies the data types and order. This is followed by one field per sample, where the data separated by two dots in that field corresponds to the specified types in the format. The first subfield should always be the genotype (GT). Summary: Variant call format (VCF) is a generic format for storing polymorphic DNA data such as SNPs, insertions, deletions, and structural variants, as well as detailed annotations. VCF is usually stored compressed and can be indexed for quick retrieval of variant data from a number of locations on the reference genome. The format was developed for the 1000 Genomes project and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merge, comparison and also a common Perl API. Each bioinformatics pipeline treats these columns differently, so you`ll need to consult with your pipeline`s subject matter experts on how best to interpret this information.
The body of VCF follows the header and is divided into 8 mandatory columns on the tab and an unlimited number of optional columns that can be used to save other sample information. If additional columns are used, the optional first column is used to describe the format of the data in subsequent columns. VCFtools is an open source software for analyzing, analyzing and editing VCF files. The software suite is roughly divided into two modules. The first module provides a common Perl API and allows you to perform various operations on VCF files, including format validation, merging, comparison, overlap, complementarity, and basic overall statistics. The second module consists of a C++ executable file that is mainly used to analyze SNP data in VCF format, allowing the user to estimate allele frequencies, degree of connection imbalance, and various quality control measures. More details about VCFtools can be found on the website (vcftools.sourceforge.net/), where the reader can also find links to alternative tools for generating and manipulating VCF, such as.B. the GATK toolkit (McKenna et al., 2010). This example shows in order a good simple SNP, a possible SNP that has been filtered because its quality is less than 10, a place where two alternative alleles are called, from which one (T) is derived (possibly a reference sequencing error), a place called a monomorphic reference (i.e.
without alternating alleles), and a microsatellite with two alternating alleles, one deletion of 3 bases (TCT) and the other an insertion of a base (A). Genotype data are given for three samples, two of which are staggered and the third is not phased accurate, with genotype, depth and haplotype qualities (the latter only for phased samples) and genotypes given per sample. Microsatellite calls are phaseless. The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics to store variations in gene sequences. The format was developed with the advent of large-scale DNA genotyping and sequencing projects such as the 1000 Genomes project. Existing formats for genetic data, such as the General Characteristics Format (GFF), stored all genetic data, many of which are redundant because they are shared between genomes. Using the variant call format, only variations should be recorded with a reference genome. VCF (Virtual Card Format) or vCard is a digital file format for storing contact information. The format is often used for data exchange between common information exchange applications. Most operating systems, such as Windows and MacOS, come with standard programs to create and open these files.
A single VCF file can contain the coordinates of one or more contacts. A VCF file typically contains information such as the contact`s name, address, phone number, email address, date of birth, photos, and audio, as well as a number of other fields. As it is supported by email clients and services, there is no data loss when transferring contacts via vCard format. The media type for the VCF file format is text/vcard. Additional genotype fields can be defined in the meta-information. However, software support for these fields cannot be guaranteed. The info column contains item-level information for this row of data and can be thought of as aggregated data that contains all the information specified at the sample level. For example, suppose we look at a location in the genome: the Number entry is an integer that describes the number of values that can be included in the INFO field.
For example, if the INFO field contains only one number, that value must be 1. However, if the INFO field describes a pair of numbers, that value must be 2, and so on. If the number of possible values varies, is unknown or unlimited, this value must be `.`. The possible types are: Integer, Float, Character, String and Flag. The `Flag` type indicates that the INFO field does not contain a value entry, and therefore the number in this case must be 0. The Description value must be enclosed in double quotation marks. Meta informationlines — Several lines prefixed by double book symbols (##). One of the main applications of next-generation sequencing is to detect variations between large populations of related samples. Recently, a next-generation playback orientation storage format has been standardized by the SAM/BAM file format specification (Li et al., 2009). .