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Fish Lake](.github/img/cover.jpg)\n\nInstall with the Conda or Mamba package manager after setting your [Bioconda channels](https://bioconda.github.io/#usage):\n\n```bash\n❯ mamba install vartovcf\n```\n\n### Features\n\n- Unlike the Perl script bundled with VarDict, this tool streams record-by-record\n- This tool is kept lean on purpose and is solely responsible for fast format conversion \n- The output is compliant with the VCF v4.2 and v4.3 specifications\n- Output VCF records are unsorted and a call to `bcftools sort` is recommended\n- At this time, only tumor-only mode (`var2vcf_valid.pl`) is supported\n\n### Example Usage\n\nReplace to call to `var2vcf_valid.pl` with `vartovcf` in a typical VarDictJava stream like:\n\n```bash\n❯ vardict-java \\\n    -b input.bam \\\n    -G hg38.fa \\\n    -N dna00001 \\\n    -c1 -S2 -E3 -g4 -f0.05 \\\n    --fisher \\\n    calling-intervals.bed \\\n  | vartovcf --reference hg38.fa --sample dna00001 \\\n  | bcftools sort -Oz \u003e variants.vcf.gz\n```\n\n### Benchmarks\n\n```bash\n❯ vartovcf --reference hs38DH.fa --sample dna00001 \u003c test.var \u003e /dev/null\n[2025-10-21T01:16:49Z INFO  vartovcf] Input stream: STDIN\n[2025-10-21T01:16:49Z INFO  vartovcf] Output stream: STDOUT\n[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 60181 variant records\n\n❯ hyperfine --warmup 5 'vartovcf -r hs38DH.fa -s dna00001 \u003c test.var \u003e /dev/null'\nBenchmark #1: vartovcf -r /references/hs38DH.fa -s dna00001 \u003c test.var \u003e /dev/null\n  Time (mean ± σ):     174.7 ms ±   1.5 ms    [User: 165.7 ms, System: 8.0 ms]\n  Range (min … max):   173.2 ms … 178.2 ms    16 runs\n\n❯ hyperfine --warmup 5 'var2vcf_valid.pl -N dna00001 -f 0.0 -E \u003c test.var \u003e /dev/null'\nBenchmark #1: var2vcf_valid.pl -N dna00001 -f 0.0 -E \u003c test.var \u003e /dev/null\n  Time (mean ± σ):     359.4 ms ±   2.5 ms    [User: 329.2 ms, System: 25.8 ms]\n  Range (min … max):   356.1 ms … 363.6 ms    10 runs\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclintval%2Fvartovcf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclintval%2Fvartovcf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclintval%2Fvartovcf/lists"}