Live briefing
Everything about Variant Call Format
File format for genomic variation data
The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects. VCF is a common output format for variant calling programs due to its relative simplicity and scalability. Many tools have been developed for editing and manipulating VCF files, including VCFtools, which was released in conjunction with the VCF format in 2011, and BCFtools, which was included as part of SAMtools until being split into an independent package in 2014. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: Variant Call FormatA 5-minute orientation
- Skim a recent paper: Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIRInfluential work since 2022
- Pick up a classic book: Cartesian meditationsThe most-reprinted book on the subject
- Read the landmark paper: The variant call format and VCFtoolsCited 16,611 times
- Go sideways: SAM (file format)A closely related topic
- Go sideways: BGZFA closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
The variant call format and VCFtools
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
vcfr : a package to manipulate and visualize variant call format data in R
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
The variant call format provides efficient and robust storage of GWAS summary statistics
SeqArray—a storage-efficient high-performance data format for WGS variant calls
VCF-kit: assorted utilities for the variant call format
🆕 Influential since 2022
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data
vcfpp: a C++ API for rapid processing of the variant call format
FSTest: an efficient tool for cross-population fixation index estimation on variant call format files
SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format
📚 Books worth reading
Cartesian meditationsEdmund Husserl, Dorion Cairns · 1960
The Bible, its meaning and supremacyFrederic William Farrar · 1897
Social work practice with transgender and gender variant youthGerald P. Mallon · 2009
Art since 1900Hal Foster, Rosalind E. Krauss · 2004- 📕The Ultimate Question of Programming, Refactoring, and EverythingAndrey Karpov · 2016
A Heritage of Open Air Square Temple Discovered In Russia · 2010
Quest for the Historical Jesus Christ and ChristianityMr.Avinash Patra · 2011
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
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- Ensembl Genomes Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species. The project is run by the European Bioinformatics Institute…
- BAM (file format) The BAM file format (which stands for Binary Alignment Map) is the lossless, compressed binary representation of a Sequence Alignment Map file. It is compressed…
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