generated: '2026-09-04'
method: searched
source: https://github.com/watchmaker-genomics/TVC (README.md on main, read 2026-09-04)
note: >-
  Watchmaker Genomics ships one first-party command-line tool. It is a bioinformatics binary, not
  an API client — it does not call any Watchmaker endpoint, and no CLI exists for the storefront
  APIs. Recorded because it is a real, versioned, documented command surface the company
  publishes and maintains.
name: TVC — TAPS+ Variant Caller
binary: tvc
language: Rust
license: LGPL-3.0
repository: https://github.com/watchmaker-genomics/TVC
version: v1.1.1
released: '2026-08-13'
calls_api: false
install:
- method: binary
  source: https://github.com/watchmaker-genomics/TVC/releases
  platforms: [macOS, Linux]
  note: Precompiled binaries published per release.
- method: container
  command: 'docker pull public.ecr.aws/e5r9o8m6/watchmakergenomics/tvc:latest'
  run: 'docker run -it --rm public.ecr.aws/e5r9o8m6/watchmakergenomics/tvc:latest -h'
  note: amd64 only. The README's -it flag is there so the progress bar renders.
- method: source
  command: 'docker build -t tvc ./'
  note: >-
    Building from source requires Git LFS (`git lfs install`, then `git lfs pull`) — test assets
    are LFS-tracked and the README says development cannot proceed without it.
usage: 'tvc [OPTIONS] <INPUT_REF> <INPUT_BAM> <OUTPUT_VCF>'
arguments:
- {name: INPUT_REF, required: true, description: Reference FASTA file (must be indexed, .fai)}
- {name: INPUT_BAM, required: true, description: 'Aligned and indexed BAM file (.bai, must carry NM tags)'}
- {name: OUTPUT_VCF, required: true, description: Output VCF path}
options:
- {flag: '-b, --min-bq', arg: MIN_BQ, default: '20', description: Minimum base quality for considering a read position}
- {flag: '-m, --min-mapq', arg: MIN_MAPQ, default: '1', description: Minimum mapping quality}
- {flag: '-d, --min-depth', arg: MIN_DEPTH, default: '2', description: Minimum depth required to make a genotype call}
- {flag: '-e, --end-of-read-cutoff', arg: END_OF_READ_CUTOFF, default: '5', description: Ignore bases within this distance from the end of the read for SNP calling}
- {flag: '-i, --indel-end-of-read-cutoff', arg: INDEL_END_OF_READ_CUTOFF, default: '20', description: Ignore bases within this distance from read ends when calling indels}
- {flag: '-x, --max-mismatches', arg: MAX_MISMATCHES, default: '10', description: Maximum allowed mismatches in an alignment for inclusion}
- {flag: '-a, --min-ao', arg: MIN_AO, default: '2', description: Minimum alternate observations required for a variant call}
- {flag: '-t, --num-threads', arg: NUM_THREADS, default: '4', description: Number of threads to use}
- {flag: '-c, --chunk-size', arg: CHUNK_SIZE, default: '1000000', description: Number of reference bases processed per thread batch}
- {flag: '-p, --error-rate', arg: ERROR_RATE, default: '0.005', description: Estimated per-base sequencing error rate used for binomial modeling}
- {flag: '-r, --stranded_read', arg: READ_NUMBER, default: r1, description: 'The read that is in the same orientation as the molecule (r1/r2)'}
- {flag: '-l, --log-level', arg: LOG_LEVEL, default: info, description: 'One of error, warn, info, debug, trace'}
- {flag: '-h, --help', description: Print help message}
example: |
  tvc \
      -t 8 \
      reference.fa \
      sample.bam \
      output.vcf
constraints:
- TVC assumes diploid genotypes.
- >-
  TVC assumes R1 or R2 shares the orientation of the original molecule; adapters that do not
  preserve orientation (AB adapters) are not supported.
- Reference and BAM must be indexed and BAMs must carry NM tags (default from BWA-MEM, Bowtie2).
related:
- {name: taps-foundry, url: 'https://github.com/watchmaker-genomics/taps-foundry', note: 'Companion methylation scripts, linked from the TVC README.'}
- {name: TVC benchmarking notebook, url: 'https://github.com/watchmaker-genomics/TVC/blob/main/analysis/TVC_benchmarking.ipynb', note: 'F1 scores on a demo data set, published in-repo.'}