/genomics-vcf-operations

name: genomics-vcf-operations
description: Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL /
  COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when calling variants from BAM (run an external caller first); adding functional annotations (use genomics-variant-annotation).
trigger: VCF, bcftools, variant filter, merge VCF
tags:
- genomics
- vcf
- bcftools
- filter
- ti-tv
- snv
- indel

genomics-vcf-operations

When to use

Load this skill for the file-based analysis named in the description. The function library and CLI share the same calculations; no external aligner, assembler, caller or annotation service is started.

Use from a step

from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("genomics-vcf-operations")
data = read_input("input.vcf", reader=library.read_records)
result = library.analyze(data)
write_output(result, "tables/result.csv")
write_output(library.distribution_figure(result), "figures/distribution.png")

Run `examples/example_step.py` through the step runner for a small, hand-worked synthetic fixture. It asserts known summary values. The reader materializes the input in memory; use bounded FASTQ reads or pre-filter large genomic files before loading them.

API

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`read_records(path: str | Path) -> pd.DataFrame`

Read records through read_input(path, reader=library.read_records).

:param path: Input file in the format documented under Inputs and outputs.

:returns: Parsed records as a DataFrame. :raises ValueError: Input values or file structure cannot be parsed.

`analyze(data: pd.DataFrame, *, min_qual: float=0.0, min_dp: int=0) -> pd.DataFrame`

Compute vcf-operations summaries and return a new table, leaving data unchanged.

:param data: Records containing chrom, pos, ref, alt, qual, filter, dp, type. :param min_qual: CLI default 0 keeps all QUAL values; raise to filter. :param min_dp: CLI default 0 keeps all INFO/DP values; FORMAT/DP is ignored. :returns: Result table with diagnostics and summary in attrs['run_info']. :raises ValueError: Required columns are absent or records are empty or invalid.

`run_info(data: pd.DataFrame, *, keep: bool=True) -> dict`

Return analysis diagnostics and summary.

:param data: Result returned by analyze. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Independent diagnostics dictionary. :raises ValueError: analyze has not populated diagnostics.

`distribution_figure(data: pd.DataFrame)`

Plot qual values without writing files.

:param data: Result table containing qual. :returns: Matplotlib Figure. :raises ValueError: The value column is absent or table is empty.

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Methods and parameters

`analyze` returns a new DataFrame and leaves the input unchanged. `run_info(result)` returns the summary and method diagnostics. The CLI passes `keep=False` so diagnostics do not enter output tables. All calculations are deterministic; synthetic CLI demos retain seed 42.

Gotchas

• `analyze` filters INFO/DP, not per-sample FORMAT/DP. Missing INFO/DP is treated as zero; each ALT becomes one row.
• `read_records` preserves VCF header lines in attrs["vcf_headers"]. The legacy CLI filtered.vcf retains DP only and replaces sample genotypes with missing values; do not use it for genotype-preserving filtering.
• `analyze` raises ValueError when no records pass filters, instead of the old CLI failing later with a missing summary key.

Inputs and outputs

Input files:

• File types: `.vcf`
• VCF structure: `##fileformat`; columns: `#CHROM`, `POS`, `ID`, `REF`, `ALT`, `QUAL`, `FILTER`, `INFO`

CLI output files:

• `tables/variants.csv`
• `filtered.vcf`
• `report.md`
• `result.json`
• Produces artifact `genomics.filtered_variants` as `filtered.vcf` (`vcf`)

The library writes no files. Steps use `write_output`; the CLI owns the listed artifacts. Public figure functions return matplotlib Figures and do not add new CLI outputs.

CLI

python skills/genomics/genomics-vcf-operations/genomics_vcf_operations.py --input input_file --output results/
python skills/genomics/genomics-vcf-operations/genomics_vcf_operations.py --demo --output /tmp/genomics_vcf_operations_demo

See also

• `references/parameters.md`
• `references/methodology.md`
• `references/output_contract.md`

Dependencies

`numpy`, `pandas`, `matplotlib`