Install vcfanno with Homebrew, apt

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

Commands and aliases

• vcfanno

Project history

The first GitHub release, v0.0.1, was published on April 29, 2015. Early 2015 releases quickly added support for annotating variant ends, BED files, custom scripting, and an API, which matches the project's focus on flexible annotation rather than a fixed database.

Pedersen, Layer, and Quinlan published the vcfanno software paper in Genome Biology on June 1, 2016. The paper framed the problem as integrating genome annotations from diverse file formats and described vcfanno as extracting and summarizing attributes from multiple annotation files into the INFO column of the original VCF.

Adoption history

The Genome Biology paper reported strong performance on whole-genome annotation workloads, including roughly 85,000 variants per second with 50 attributes from 17 commonly used annotation resources. That performance claim helped establish vcfanno as a practical tool for large human variant datasets as well as non-human species.

The project README asks users to cite the paper and shows active maintenance through many GitHub releases, including v0.3.9 in June 2026. It is also packaged by Bioconda and distribution package managers, which places it in the standard bioinformatics command-line ecosystem.

How it is used

Users write a TOML configuration with one or more `[[annotation]]` blocks that name source files, fields or columns, operations, and output INFO names. vcfanno then streams a query VCF and writes an annotated VCF, commonly with `-p` for parallelism and optional Lua scripts for custom reductions.

Common tasks include overlaying population allele frequencies, conservation scores, ClinVar or ExAC-like annotations, BED-derived regional scores, BAM-derived coverage summaries, and structural-variant endpoint annotations onto a study VCF before filtering or interpretation.

Why package nerds care

vcfanno matters to package people because it turns a pile of tabix-indexed genomics resources into a reproducible, reviewable config file and one CLI invocation. That is exactly the shape package managers like: a small binary that composes with bgzip/tabix, pipes, VCF validators, and downstream filters.

It also represents the post-VCF-standard tooling wave: once VCF became the lingua franca, the hard day-to-day problem shifted to attaching the right outside evidence to millions of variants quickly and repeatably.

Timeline

• 2015-04-29: vcfanno v0.0.1 is published as the initial GitHub release.
• 2015-05-04: v0.0.2 adds support for annotating ends of variants such as CNVs and SVs.
• 2016-06-01: The Genome Biology vcfanno paper is published.
• 2026-06-16: GitHub lists v0.3.9 as the latest release.

Related projects

• VCFtools and HTSlib provide the broader VCF and indexed-file ecosystem that vcfanno workflows build on.
• vcflib is a companion VCF-processing toolkit; the 2022 vcflib paper also points to vcfanno as a related tool for adding annotations from VCFs and BED files.
• GATK, FreeBayes, ExAC-style resources, ClinVar-style resources, and tabix-indexed annotation files are common upstream or companion inputs in vcfanno pipelines.

Sources

• https://api.github.com/repos/brentp/vcfanno/releases
• https://github.com/brentp/vcfanno
• https://link.springer.com/article/10.1186/s13059-016-0973-5
• https://pubmed.ncbi.nlm.nih.gov/27250555/