vartriage 0.4.0

A streaming pipeline library for identifying and classifying pathogenic genetic variants from VCF data

vartriage

Variant prioritization pipeline for whole-genome sequencing data. Takes a VCF, applies quality filters, annotates functional consequence and population frequency, scores pathogenicity via CADD/REVEL/SpliceAI, runs ACMG/AMP evidence classification, and outputs a ranked candidate list.

Benchmarks:

Workload	Variants	Wall time	Peak RSS	Throughput
GIAB HG002 (QC only, no annotation)	4,048,342	156 s	122 MB	~26K var/sec
chr22 full annotation (GENCODE + 4.8M gnomAD)	130,141	36.3 s	~2 GB	~3.6K var/sec
chr22 annotation (100K gnomAD subset)	130,141	19.5 s	453 MB	~6.7K var/sec

Streaming architecture, so JSON and CSV reports never buffer the full variant set in memory. Reference files (GTF, CADD, REVEL, SpliceAI) are cached after first parse. Subsequent runs load from cache in seconds.

Install

pip install vartriage

Optional extras:

pip install vartriage[accelerated]   # polars + pyranges backends
pip install vartriage[pdf]           # reportlab PDF reports
pip install vartriage[all]           # everything

CLI

vartriage --vcf sample.vcf.gz --output candidates.json

Full options:

vartriage \
  --vcf sample.vcf.gz \
  --output report.json \
  --output-format json \
  --gene-annotation gencode.v44.gtf \
  --gnomad gnomad.v4.sites.tsv \
  --clinvar clinvar_20240101.tsv \
  --cadd-scores cadd_scores.tsv \
  --revel-scores revel_scores.tsv \
  --spliceai-scores spliceai_scores.tsv \
  --gene-list my_panel.txt \
  --regions target_regions.bed \
  --sample PROBAND_01 \
  --min-gq 20

Run vartriage --help for the complete list.

Python API

Run the whole pipeline:

from pathlib import Path
from vartriage import (
    Pipeline, PipelineConfig, AnnotationConfig,
    PrioritizationConfig, QualityFilterConfig, ReportConfig,
)

config = PipelineConfig(
    vcf_path=Path("sample.vcf.gz"),
    output_path=Path("candidates.json"),
    quality_filter=QualityFilterConfig(min_qual=30.0),
    annotation=AnnotationConfig(
        gene_annotation_path=Path("gencode.v44.gtf"),
        gnomad_path=Path("gnomad.v4.sites.tsv"),
        clinvar_path=Path("clinvar_20240101.tsv"),
    ),
    prioritization=PrioritizationConfig(
        max_allele_frequency=0.01,
        cadd_scores_path=Path("cadd_scores.tsv"),
        revel_scores_path=Path("revel_scores.tsv"),
    ),
    report=ReportConfig(output_format="json"),
)

pipeline = Pipeline(config)
pipeline.run()

Or use stages individually:

from vartriage import VCFParser, QualityFilter, QualityFilterConfig

with VCFParser(Path("input.vcf.gz")) as parser:
    qf = QualityFilter(QualityFilterConfig(min_qual=30.0))
    for variant in qf.apply(iter(parser)):
        print(f"{variant.chrom}:{variant.pos} {variant.ref}>{variant.alt}")

Pipeline stages

VCFParser → [SampleExtractor] → [RegionFilter] → QualityFilter → AnnotationEngine → [GeneFilter] → PrioritizationEngine → ACMGClassifier → ReportGenerator

Stages in brackets are optional and activate based on config.

Sample extraction (--sample) - Pulls a single sample from multi-sample VCFs. Only variants where the named sample carries an alternate allele are kept. Optional --min-gq threshold drops low-confidence genotype calls.

Region filtering (--regions) - Restricts to variants overlapping intervals in a BED file. Useful for gene panel target regions.

Quality filtering - Drops variants where FILTER isn't PASS/., QUAL is below threshold (default 20), or QUAL is missing entirely.

Annotation - Adds functional consequence (from GTF gene models), population frequency (gnomAD), and ClinVar significance. Multiple-transcript conflicts resolve to the most damaging consequence. Consequence severity: Frameshift > Nonsense > Splice_Site > Missense > In_Frame_Insertion > In_Frame_Deletion > Synonymous > Intergenic.

Gene filtering (--gene-list) - After annotation, restricts to variants in genes from a user-supplied text file. Case-insensitive matching. Logs a warning for any panel genes with zero hits (catches typos).

Prioritization - Two phases. First: frequency gate drops variants with AF above the threshold (default 0.01); unknown-frequency variants always pass. Second: composite scoring from normalized CADD Phred, REVEL, and SpliceAI:

composite = (REVEL × 0.5) + (CADD_normalized × 0.3) + (SpliceAI × 0.2)

When only two scores are available, weights redistribute proportionally. Single available score is used directly. Falls back to the legacy two-score formula (0.6/0.4) when SpliceAI is not configured.

ACMG classification - Tags evidence per ACMG/AMP 2015 guidelines:

Tag	Condition
PVS1	Nonsense, Frameshift, or Splice_Site + SpliceAI > 0.8
PM2	gnomAD AF < 0.0001
PP3	REVEL > 0.7 or SpliceAI > 0.5 on splice-adjacent
PP5	ClinVar Pathogenic without conflicting Benign

Tags combine into Pathogenic, Likely_Pathogenic, or VUS. Missing data sources mean the tag is simply omitted.

Report output - JSON and CSV stream directly from the iterator (no buffering). PDF materializes for page layout. VCF re-reads the source file, injects VARTRIAGE_* INFO fields for classified variants, and writes bgzipped output with a tabix index. Output fields: chromosome, position, ref/alt alleles, functional consequence, allele frequency, composite rank, ClinVar assertion, ACMG classification, evidence tags.

Configuration

QualityFilterConfig

Field	Type	Default	Range
min_qual	float	20.0	0-1,000,000

AnnotationConfig

Field	Type	Default	Notes
gene_annotation_path	Path	required	GTF/GFF
gnomad_path	Path	required	TSV or tabix VCF (.vcf.bgz/.vcf.gz)
clinvar_path	Path	None	TSV
batch_size	int	10,000	1,000-100,000

PrioritizationConfig

Field	Type	Default	Notes
max_allele_frequency	float	0.01	0.0-1.0
cadd_scores_path	Path	None	CADD Phred TSV
revel_scores_path	Path	None	REVEL TSV
spliceai_scores_path	Path	None	SpliceAI TSV
batch_size	int	10,000	1,000-100,000

ReportConfig

Field	Type	Default	Options
output_format	str	"json"	"json", "csv", "pdf", "vcf"

GeneFilterConfig

Field	Type	Default	Notes
gene_list_path	Path	required	Plain text, one gene symbol per line

RegionFilterConfig

Field	Type	Default	Notes
bed_path	Path	required	BED file with target intervals

SampleConfig

Field	Type	Default	Notes
sample_name	str	required	Sample name from VCF header
min_gq	int	None	Genotype quality threshold (0-99)

Reference file formats

All TSV with a header row. Tab-separated.

Gene list - Plain text file, one gene symbol per line. Comment lines starting with # are ignored. Blank lines are skipped. Symbols are matched case-insensitively.

# Cardiac panel v2
BRCA1
BRCA2
TP53
MLH1

gnomAD (TSV) - columns: chrom, pos, ref, alt, af. The value '.' in the af column is treated as null (gnomAD compatibility).

gnomAD (tabix VCF) - bgzipped VCF with a .tbi index (.vcf.bgz or .vcf.gz). When you point gnomad_path at a tabix-indexed file, vartriage queries it on the fly with zero memory overhead for the reference. Useful when your gnomAD file is too large to fit in RAM as a dict.

ClinVar - columns: chrom, pos, ref, alt, clinical_significance. Values: Pathogenic, Likely pathogenic, Uncertain significance, Likely benign, Benign.

CADD / REVEL / SpliceAI - columns: chrom, pos, ref, alt, score. Lines starting with # are skipped. All three use the same TSV format.

Missing data handling

Variants absent from gnomAD are never dropped; they get frequency_unknown=True and pass the frequency filter. Same for ClinVar: no match means clinvar_unknown=True.

A MissingDataWarning fires per lookup miss. After a run:

acc = pipeline.warning_accumulator
print(f"{acc.total_count} missing data events across {acc.sources}")

Warning hierarchy

All warnings inherit from VarTriageWarning (a UserWarning subclass). Silence everything at once:

import warnings
from vartriage import VarTriageWarning
warnings.filterwarnings("ignore", category=VarTriageWarning)

Dependencies

Package	Required	Extra	Purpose
pysam >=0.22,<1.0	yes	-	VCF streaming via htslib
numpy >=1.24,<3.0	yes	-	Score normalization
polars >=0.20,<2.0	no	[accelerated]	Batch frequency/ClinVar joins
pyranges >=0.1,<1.0	no	[accelerated]	Interval overlap queries
reportlab >=4.0,<5.0	no	[pdf]	PDF report rendering

Without optional extras, the library uses pure-Python fallbacks (dict lookups, bisect-based interval tree). Same output either way; the accelerated path is faster on large reference files.

Caching

Reference files (GTF gene models, CADD scores, REVEL scores, SpliceAI scores) are parsed once and cached as pickle files adjacent to the source (with a .vartriage.cache suffix). On subsequent runs, the cache loads in seconds instead of re-parsing.

Cache invalidation is automatic: if the source file's mtime changes or the vartriage version changes, the cache rebuilds. Writes are atomic (temp file + rename), so a crash mid-write won't corrupt anything.

To force a fresh parse, delete the .vartriage.cache file next to your reference.

Type checking

The package ships a py.typed marker (PEP 561). All protocol return types are fully typed, with no Any in the annotation engine interfaces.

mypy --strict vartriage/

Tests

pytest tests/                     # full suite
pytest tests/ -m "not slow"       # skip benchmarks

CI

GitHub Actions runs on Python 3.10, 3.11, and 3.12. PyPI publishing uses trusted publisher (no token in secrets).

Project layout

vartriage/
    cli.py                # CLI entry point
    pipeline.py           # Orchestrator
    protocols.py          # Protocol interfaces (IntervalIndex, FrequencyDatabase, etc.)
    io/                   # VCF parsing
    filter/               # Quality, region, sample, and gene filtering
    annotation/           # Consequence, frequency, ClinVar lookups
    prioritization/       # AF gating + CADD/REVEL/SpliceAI scoring (ScoreLoader)
    classification/       # ACMG evidence tagging
    reporting/            # JSON, CSV, PDF, VCF (streaming writers)
    models/               # Dataclasses, enums, configs, warnings
    _internal/            # Batch utils, interval tree, caching, vectorized ops
    py.typed              # PEP 561 marker

Contributing

See CONTRIBUTING.md.

License

MIT