svforge 1.0.2

Synthetic VCF generator for structural variants (Manta, DELLY) with controlled variability and realistic artefact injection

Generate synthetic SV VCFs to stress-test your pipelines with confidence

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svForge produces caller-shaped VCFs (Manta, DELLY) in VCF / VCF.gz / BCF format with fine-grained control over variability (HOMLEN, SVLEN, VAF) and realistic artefact injection (SVs in ENCODE blacklist regions, gnomAD germline SVs).

Designed to be modular, it is easy to adapt to your own use case. You can tune generation parameters, plug in new callers, and customize the workflow without reworking the whole tool.

Installation

pip install svforge

Or from source:

git clone https://github.com/pieetie/svforge
cd svforge
pip install -e ".[dev,test]"

Quick start

For ready-to-run command lines (single-sample gen, paired somatic gen-pair, validation, banks, and dev checks), see docs/ready-to-use.md.

Scope & limitations

svForge ships the full header of each target caller verbatim, but for now it does not populate every INFO/FORMAT field a real run would emit. The fields below are declared in the header for parser compatibility but left empty in records — support may land in a later release.

Manta — not yet populated: CIPOS, CIEND (alignment-derived breakpoint CIs), HOMSEQ (microhomology sequence; HOMLEN is populated), BND_DEPTH, MATE_BND_DEPTH (per-breakend coverage).

DELLY — not yet populated: RDRATIO (tumor/normal read-depth ratio), INSLEN, SRMAPQ, CONSENSUS, CONSBP (split-read consensus); also, records are currently always tagged PRECISE rather than alternating with IMPRECISE.

In the meantime, if your downstream pipeline hard-requires any of these fields, you can supply your own --header-template that drops the unused declarations, or post-process the VCF to fill them with sentinel values.

Typical use cases

• Validate downstream filters (for example, SVFORGE_SOURCE=gnomad records should disappear after your gnomAD filtering step).
• Validate ENCODE blacklist annotation logic (for example, SVFORGE_SOURCE=blacklist records should receive your expected poor-mappability label).
• Run reproducible CI regression tests with fixed seeds, without committing generated VCF files.
• Smoke-test deployments and pipeline changes in seconds instead of rerunning full variant callers on BAM files.
• Reproduce specific scenarios and edge cases (cross-chrom BNDs, contig-edge events, controlled VAF/HOMLEN ranges) for debugging and QA.
• Demo or onboard safely with realistic SV VCFs and no patient data.

CLI

svforge gen          # one VCF for one sample
svforge gen-pair     # one 2-sample somatic VCF (NORMAL + TUMOR)
svforge validate     # self-consistency check of injected SVs
svforge bank list    # list built-in banks
svforge bank show    # dump a bank as YAML
svforge callers      # list registered writers

Run svforge <cmd> --help for the full flag list.

Credits

• Logo and visual identity - Elisa Perrin
• Claude (Anthropic) - assisted with tests, documentation, refactoring, and release tooling (Ruff linting/formatting, CI cleanup)

License

Distributed under the MIT License.