How acenglish/truvari works
Truvari is a command-line toolkit for structural-variant VCF comparison, benchmarking, merging, harmonization, and annotation. Its main workflow takes base and comparison VCFs through benchmarking to performance results; users can then refine benchmark results with phab. Other documented commands provide independent analysis branches. The graph preserves these capabilities and the shared variant-processing layer. Command implementations are represented by their documented modules; source excerpts were partial, so uncertain internal call wiring is omitted.
Main entry points: __main__.py Command dispatcher · variant_file.py VCF access · phab.py Harmonize variants · comparisons.py Benchmark VCFs
Components 24
Command workflows
- Command dispatcher
truvari/__main__.py
Comparison and benchmarking
- Benchmark VCFs
truvari/comparisons.py - Match variants
truvari/matching.py - Benchmark results
truvari/comparisons.py
Variant processing
- Variant parameters
truvari/variant_params.py - Variant records
truvari/variant_record.py - VCF access
truvari/variant_file.py - Variant utilities
truvari/utils.py
Merging and harmonization
- Collapse variants
truvari/collapse.py - Refine results
truvari/refine.py - Harmonize variants
truvari/phab.py - Consolidate results
truvari/make_ga4gh.py
Annotation and analysis
- Annotate VCF
truvari/anno.py - Annotation methods
truvari/annotations - Consistency report
truvari/consistency.py - VCF to DataFrame
truvari/vcf2df.py - Segment variants
truvari/segmentation.py - Region counts
truvari/stratify.py - Shard VCF
truvari/divide.py - MSA to VCF
truvari/msatovcf.py
Other components
- User
- Input VCFs
- Reference FASTA
- Output VCF
Connections 38
- User → Command dispatcher: runs commands
- Command dispatcher → Benchmark VCFs: dispatches
- Command dispatcher → Collapse variants: dispatches
- Command dispatcher → Refine results: dispatches
- Command dispatcher → Harmonize variants: dispatches
- Command dispatcher → Consolidate results: dispatches
- Command dispatcher → Annotate VCF: dispatches
- Command dispatcher → Consistency report: dispatches
- Command dispatcher → VCF to DataFrame: dispatches
- Command dispatcher → Segment variants: dispatches
- Command dispatcher → Region counts: dispatches
- Command dispatcher → Shard VCF: dispatches
- Input VCFs → VCF access: read VCFs
- Benchmark VCFs → VCF access: reads variants
- Benchmark VCFs → Match variants: matches variants
- Benchmark VCFs → Benchmark results: writes metrics
- Match variants → Variant records: compares records
- VCF access → Variant records: yields records
- Variant parameters → Variant records: configures
- Reference FASTA → Harmonize variants: builds haplotypes
- Harmonize variants → Input VCFs: reads variants
- Refine results → Harmonize variants: uses harmonization
- Refine results → Benchmark results: refines results
- Collapse variants → VCF access: reads variants
- Collapse variants → Match variants: checks matches
- Collapse variants → Output VCF: writes collapsed calls
- Harmonize variants → Output VCF: writes harmonized calls
- Annotate VCF → Annotation methods: applies annotations
- Annotate VCF → VCF access: reads variants
- Annotation methods → Reference FASTA: uses reference
- Annotate VCF → Output VCF: writes annotated calls
- Consistency report → VCF access: reads VCFs
- VCF to DataFrame → VCF access: reads variants
- Segment variants → VCF access: reads variants
- Region counts → VCF access: counts regions
- Shard VCF → VCF access: reads variants
- Consolidate results → Benchmark results: consolidates results
- MSA to VCF → Output VCF: writes VCF