install

Additional install commands

macOS

Homebrewverified · 100%

brew install echtvar

local Homebrew formula metadata

overview

Package summary

Rapid variant annotation and filtering

Project links

Commands and aliases

echtvar

history

Project history and usage

echtvar is a Rust command-line tool for rapid genomic variant annotation and filtering. Its package relevance is specialized but clear: it turns large population VCF resources into compact searchable archives that can annotate cohort VCF/BCF files quickly.

Project history

The public repository was created in November 2021, and the first GitHub release, v0.1.0, was published in January 2022. The README describes echtvar as efficiently encoding variant allele frequency and other information from huge population datasets for rapid annotation at about one million variants per second.

The project is backed by a Nucleic Acids Research article and is developed in the Jeroen de Ridder lab. Its README explains the core design: chunking the genome, encoding variants into compact integers when possible, using zip files, delta encoding, integer compression, and lookup tables for selected integer, float, or low-cardinality string fields.

Adoption history

echtvar's adoption path is a scientific-tool path rather than a broad developer-tool path: users can download static binaries and pre-encoded gnomAD v3.1.2 resources from GitHub releases, or build the Rust project themselves. Homebrew packaging makes it easier to install the executable on developer and analysis workstations.

The project is niche compared with general bioinformatics standards such as htslib, but it fills a practical need for fast annotation/filtering against large population datasets.

How it is used

A common workflow is to encode a population VCF once with echtvar encode, then reuse the resulting .echtvar.zip archive for many annotation runs with echtvar anno. The README shows annotation with multiple -e archive arguments and optional filtering expressions such as allele-frequency thresholds.

Encode configuration uses JSON5 to select and rename VCF fields, while annotation consumes decomposed and normalized VCF/BCF inputs and can stream from stdin.

Why package nerds care

echtvar is interesting because it packages a paper-backed bioinformatics data structure as a small Rust CLI. Package managers help users get the executable, while GitHub releases carry large precomputed domain data that would not belong inside a formula.

Its dependency story is also typical of modern bioinformatics packaging: htslib/rust-htslib for VCF/BCF I/O, compression libraries for speed, and a command-line interface meant to slot into pipelines.

Timeline

2021: Public echtvar GitHub repository created.
2022: v0.1.0 initial release published.
2022: Nucleic Acids Research article page published for echtvar.
2026: v0.2.4 released, with repository activity continuing.

Related projects

The README credits htslib via rust-htslib for reading and writing BCF/VCF.
gnomAD is the main example population resource used for pre-encoded echtvar archives.
stream-vbyte, bincode, and fasteval are part of the implementation and expression-evaluation story described by the README.

Sources

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

narrow executable package without higher-risk signals

Signals

metadata:no-higher-risk-signals

Install behavior

No Homebrew post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 1 runtime dependencies.
Build metadata lists 3 build dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

Command	Kind	Exposure	Note
`echtvar`	cli	global executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08

manager version0.2.4

manager updated2026-04-30

local dataok

upstreamcurrent

latest detectedv0.2.4

https://github.com/brentp/echtvar

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:echtvar
Version	0.2.4
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/echtvar
Homepage	https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac931/6775383
Repository	https://github.com/brentp/echtvar
Upstream docs	https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac931/6775383
License	MIT
Source archive	https://github.com/brentp/echtvar/archive/refs/tags/v0.2.4.tar.gz
Last updated	2026-04-30T17:38:56Z
Pulse	updated
Dependencies	openssl@3
Build dependencies	cmake, pkgconf, rust
Uses from macOS	bzip2
Bottle	available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	not defined
Service	none declared

registry facts

Source database details

Source Database	Homebrew formula API
Tap	homebrew/core
Full Name	echtvar
Version Scheme	0
Revision	0
Bottle Stable Root URL	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Combined YAML source

View the package source record on GitHub.

combined/echtvar.yml

Used sources

Geiger risk classifier
Nucleus package database
av.db category and tag curation
cross-ecosystem install command graph
curated package history
package relationship graph
package version freshness
package-page enrichment

Install echtvar with Homebrew