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brentp committed Jun 14, 2022
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## Echtvar: Really, truly rapid variant annotation and filtering
[![Rust](https://github.com/brentp/echtvar/actions/workflows/ci.yml/badge.svg)](https://github.com/brentp/echtvar/actions/workflows/ci.yml)

Echtvar enables rapid variant annotation and filtering with huge pupulation datasets
Echtvar efficiently encodes variant allele frequency and other information from huge pupulation datasets to enable rapid (1M variants/second) annotation of genetic variants.
It chunks the genome into 1<<20 (~1 million) bases,
[encodes each variant into a 32 bit integer](https://github.com/brentp/echtvar/blob/02774b8d1cd3703b65bd2c8d7aab93af05b7940f/src/lib/var32.rs#L9-L21) (with a [supplemental table](https://github.com/brentp/echtvar/blob/02774b8d1cd3703b65bd2c8d7aab93af05b7940f/src/lib/var32.rs#L33-L38)
for those that can't fit due to large REF and/or ALT alleles). It uses the zip format, [delta
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to create a compact and searchable format of any integer, float, or low-cardinality string columns
selected from the population file.

An echtvar (zip) file can be used to annotate and filter variants in a VCF (or
BCF) file at a rate of >1 million variants per second (most of the time is spent
reading and writing VCF/BCF, so this number depends on the particular file).

read more at the [why of echtvar](https://github.com/brentp/echtvar/wiki/why)

### Getting started.
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That page contains exact instructions to get started with the static binary.

<details>
<summary>:arrow_down:Download instructions for linux</summary>
<summary>:arrow_down:Download or Build instructions for linux</summary>

The linux binary is available via:

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