https://github.com/clintval/vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.
https://github.com/clintval/vartovcf

bioinformatics rust variant-calling

Last synced: 4 months ago
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Convert variants from VarDict/VarDictJava into VCF v4.2 format.

• Host: GitHub
• URL: https://github.com/clintval/vartovcf
• Owner: clintval
• License: mit
• Created: 2021-01-24T05:19:07.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2025-12-18T20:22:32.000Z (6 months ago)
• Last Synced: 2025-12-21T08:08:57.658Z (6 months ago)
• Topics: bioinformatics, rust, variant-calling
• Language: Rust
• Homepage:
• Size: 1.8 MB
• Stars: 5
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# vartovcf

[![Install with bioconda](https://img.shields.io/badge/Install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/recipes/vartovcf/README.html)

[![Anaconda Version](https://anaconda.org/bioconda/vartovcf/badges/version.svg)](http://bioconda.github.io/recipes/vartovcf/README.html)

[![Build Status](https://github.com/clintval/vartovcf/actions/workflows/rust.yml/badge.svg?branch=main)](https://github.com/clintval/vartovcf/actions/workflows/rust.yml)

[![Coverage Status](https://coveralls.io/repos/github/clintval/vartovcf/badge.svg?branch=main)](https://coveralls.io/github/clintval/vartovcf?branch=main)

[![Language](https://img.shields.io/badge/language-rust-a72144.svg)](https://www.rust-lang.org/)

Convert variants from VarDict/VarDictJava into VCF v4.2 format.

![The Pacific Northwest - Fish Lake](.github/img/cover.jpg)

Install with the Conda or Mamba package manager after setting your [Bioconda channels](https://bioconda.github.io/#usage):

```bash

❯ mamba install vartovcf

```

### Features

- Unlike the Perl script bundled with VarDict, this tool streams record-by-record

- This tool is kept lean on purpose and is solely responsible for fast format conversion 

- The output is compliant with the VCF v4.2 and v4.3 specifications

- Output VCF records are unsorted and a call to `bcftools sort` is recommended

- At this time, only tumor-only mode (`var2vcf_valid.pl`) is supported

### Example Usage

Replace to call to `var2vcf_valid.pl` with `vartovcf` in a typical VarDictJava stream like:

```bash

❯ vardict-java \

    -b input.bam \

    -G hg38.fa \

    -N dna00001 \

    -c1 -S2 -E3 -g4 -f0.05 \

    --fisher \

    calling-intervals.bed \

  | vartovcf --reference hg38.fa --sample dna00001 \

  | bcftools sort -Oz > variants.vcf.gz

```

### Benchmarks

```bash

❯ vartovcf --reference hs38DH.fa --sample dna00001 < test.var > /dev/null

[2025-10-21T01:16:49Z INFO  vartovcf] Input stream: STDIN

[2025-10-21T01:16:49Z INFO  vartovcf] Output stream: STDOUT

[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 60181 variant records

❯ hyperfine --warmup 5 'vartovcf -r hs38DH.fa -s dna00001 < test.var > /dev/null'

Benchmark #1: vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null

  Time (mean ± σ):     174.7 ms ±   1.5 ms    [User: 165.7 ms, System: 8.0 ms]

  Range (min … max):   173.2 ms … 178.2 ms    16 runs

❯ hyperfine --warmup 5 'var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null'

Benchmark #1: var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null

  Time (mean ± σ):     359.4 ms ±   2.5 ms    [User: 329.2 ms, System: 25.8 ms]

  Range (min … max):   356.1 ms … 363.6 ms    10 runs

```