Variant Analysis and Annotation

Production-ready VCF processing and variant annotation skill combining local bioinformatics computation with ToolUniverse database integration. Designed to answer bioinformatics analysis questions about VCF data, mutation classification, variant filtering, and clinical annotation.

Domain Reasoning

VCF quality filtering must come before interpretation. A variant called at 2x read depth is unreliable regardless of its QUAL score, because stochastic sequencing errors at low depth can mimic true variants. The recommended minimums — depth > 10x, QUAL > 20, allele frequency consistent with expected zygosity — are not conservative; they are the floor below which calls cannot be trusted. Applying lenient filters to "keep more variants" sacrifices accuracy for coverage and produces false positives that propagate through all downstream analyses.

LOOK UP DON'T GUESS

• Clinical significance of specific variants: query MyVariant_query_variants or EnsemblVEP_annotate_rsid; never cite ClinVar classifications from memory.
• Population allele frequencies: retrieve from MyVariant.info or gnomAD tools; do not assume rarity.
• ClinGen dosage sensitivity scores for genes in a CNV: call ClinGen_dosage_by_gene; do not estimate HI/TS scores.
• Mutation consequence predictions: run Ensembl VEP or retrieve from MyVariant.info; do not classify impact without tool output.

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CRISPR sgRNA Design Reasoning

• PAM sequence (NGG for SpCas9) must lie 3' of the target on the non-target strand; the guide RNA targets the 20 nt immediately upstream of the PAM
• For exon targeting: choose guides that cut early in the coding sequence for maximum frameshift/disruption
• Off-target risk increases with fewer mismatches; always check for genomic sites with 0-3 mismatches to the guide

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When to Use This Skill

Triggers:

• User provides a VCF file (SNV/indel or SV) and asks questions about its contents
• Questions about variant allele frequency (VAF) filtering
• Mutation type classification queries (missense, nonsense, synonymous, etc.)
• Structural variant interpretation requests (deletions, duplications, CNVs)
• Variant annotation requests (ClinVar, gnomAD, CADD, dbSNP)
• CNV pathogenicity assessment using ClinGen dosage sensitivity
• Cohort comparison questions
• Population frequency filtering (SNVs or SVs)
• Intronic/intergenic variant filtering
• Gene dosage sensitivity queries

Example Questions:

• "What fraction of variants with VAF < 0.3 are annotated as missense mutations?"
• "After filtering intronic/intergenic variants, how many non-reference variants remain?"
• "What is the clinical significance of this deletion affecting BRCA1?"
• "Which dosage-sensitive genes overlap this 500kb duplication on chr17?"
• "How many variants have clinical significance annotations?"
• "Compare variant counts between samples"

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Core Capabilities

Capability	Description
VCF Parsing	Pure Python + cyvcf2 parsers. VCF 4.x, gzipped, multi-sample, SNV/indel/SV
Mutation Classification	Maps SO terms, SnpEff ANN, VEP CSQ, GATK Funcotator to standard types
VAF Extraction	Handles AF, AD, AO/RO, NR/NV, INFO AF formats
Filtering	VAF, depth, quality, PASS, variant type, mutation type, consequence, chromosome, SV size
Statistics	Ti/Tv ratio, per-sample VAF/depth stats, mutation type distribution, SV size distribution
Annotation	MyVariant.info (aggregates ClinVar, dbSNP, gnomAD, CADD, SIFT, PolyPhen)
SV/CNV Analysis	gnomAD SV population frequencies, DGVa/dbVar known SVs, ClinGen dosage sensitivity
Clinical Interpretation	ACMG/ClinGen CNV pathogenicity classification using haploinsufficiency/triplosensitivity scores
DataFrame	Convert to pandas for advanced analytics
Reporting	Markdown reports with tables and statistics, SV clinical reports

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Workflow Overview

Phase 1: Parse VCF → Extract CHROM/POS/REF/ALT/QUAL/FILTER/INFO, per-sample GT/VAF/depth, annotations (ANN/CSQ/FUNCOTATION). Pure Python or cyvcf2.

Phase 2: Classify → Variant type (SNV/INS/DEL/MNV/SV), mutation type (missense/nonsense/synonymous/frameshift/splice/etc.), impact (HIGH/MODERATE/LOW/MODIFIER).

Phase 3: Filter → VAF range, depth, quality, PASS, variant/mutation type, consequence exclusion, population frequency, chromosome, SV size.

Phase 4: Statistics → Type/mutation/impact/chromosome distributions, Ti/Tv ratio, per-sample VAF/depth, gene mutation counts.

Phase 5: Annotate (optional) → MyVariant.info (ClinVar/dbSNP/gnomAD/CADD), Ensembl VEP consequence prediction.

Phase 6: Report → Markdown tables, direct answers, DataFrame export.

Phase 7: SV/CNV Analysis (if applicable) → gnomAD SV frequencies, ClinGen dosage sensitivity, ACMG pathogenicity classification.

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Phase Summaries

Phase 1: VCF Parsing

Use pandas for:

• Reading VCF as structured data
• Quick exploratory analysis
• When you need to manipulate columns and rows

Use python_implementation tools for:

• Production parsing with annotation extraction
• Multi-sample VCF handling
• VAF extraction from FORMAT fields
• Large file streaming

Key functions:

vcf_data = parse_vcf("input.vcf")           # Pure Python (always works)
vcf_data = parse_vcf_cyvcf2("input.vcf")    # Fast C-based (if installed)
df = variants_to_dataframe(vcf_data.variants, sample="TUMOR")  # For pandas

Phase 2: Variant Classification

Automatic classification from annotations:

• SnpEff ANN field
• VEP CSQ field
• GATK Funcotator FUNCOTATION field
• Standard INFO keys: EFFECT, EFF, TYPE

Mutation types supported: missense, nonsense, synonymous, frameshift, splice_site, splice_region, inframe_insertion, inframe_deletion, intronic, intergenic, UTR_5, UTR_3, upstream, downstream, stop_lost, start_lost

See references/mutation_classification_guide.md for full details

Phase 3: Filtering

Common filtering patterns:

# Somatic-like variants
criteria = FilterCriteria(
    min_vaf=0.05, max_vaf=0.95,
    min_depth=20, pass_only=True,
    exclude_consequences=["intronic", "intergenic", "upstream", "downstream"]
)

# High-confidence germline
criteria = FilterCriteria(
    min_vaf=0.25, min_depth=30, pass_only=True,
    chromosomes=["1", "2", ..., "22", "X", "Y"]
)

# Rare pathogenic candidates
criteria = FilterCriteria(
    min_depth=20, pass_only=True,
    mutation_types=["missense", "nonsense", "frameshift"]
)

See references/vcf_filtering.md for all filter options

Phase 4-6: Statistics, Annotation, Reporting

Use python_implementation for standard stats (Ti/Tv, type distributions, per-sample VAF/depth); pandas for custom aggregations. For annotation, prefer MyVariant.info (batch: ClinVar + dbSNP + gnomAD + CADD); limit to 50-100 variants per batch. Reports include type/mutation/impact/chromosome distributions, VAF stats, clinical significance, and top mutated genes.

See references/annotation_guide.md for detailed examples

Phase 7: Structural Variant & CNV Analysis

When VCF contains SV calls (SVTYPE=DEL/DUP/INV/BND):

1. Identify affected genes (from VCF annotation or coordinate overlap)
2. Query ClinGen dosage sensitivity:

   clingen = ClinGen_dosage_by_gene(gene_symbol="BRCA1")
   # Returns: haploinsufficiency_score, triplosensitivity_score
   

3. Check population frequency:

   gnomad_sv = gnomad_get_sv_by_gene(gene_symbol="BRCA1")
   # Returns: SVs with AF, AC, AN
   

4. Classify pathogenicity:
   • Pathogenic: Deletion + HI score = 3, AF < 0.0001
   • Likely Pathogenic: Deletion + HI score = 2, AF < 0.001
   • VUS: HI/TS score = 0-1, AF 0.001-0.01
   • Benign: AF > 0.01

ClinGen dosage score interpretation:

• 3: Sufficient evidence for dosage pathogenicity (HIGH impact)
• 2: Some evidence (MODERATE impact)
• 1: Little evidence (LOW impact)
• 0: No evidence (MINIMAL impact)
• 40: Dosage sensitivity unlikely

See references/sv_cnv_analysis.md for full SV workflow

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Answering BixBench Questions

Pattern 1: VAF + Mutation Type Fraction

Question: "What fraction of variants with VAF < X are annotated as Y mutations?"

result = answer_vaf_mutation_fraction(
    vcf_path="input.vcf",
    max_vaf=0.3,
    mutation_type="missense",
    sample="TUMOR"
)
# Returns: fraction, total_below_vaf, matching_mutation_type

Pattern 2: Cohort Comparison

Question: "What is the difference in mutation frequency between cohorts?"

result = answer_cohort_comparison(
    vcf_paths=["cohort1.vcf", "cohort2.vcf"],
    mutation_type="missense",
    cohort_names=["Treatment", "Control"]
)
# Returns: cohorts, frequency_difference

Pattern 3: Filter and Count

Question: "After filtering X, how many Y remain?"

result = answer_non_reference_after_filter(
    vcf_path="input.vcf",
    exclude_intronic_intergenic=True
)
# Returns: total_input, non_reference, remaining

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ToolUniverse Tools Reference

SNV/Indel Annotation

Tool	When to Use	Parameters	Response
MyVariant_query_variants	Batch annotation	query (rsID/HGVS)	ClinVar, dbSNP, gnomAD, CADD
dbsnp_get_variant_by_rsid	Population frequencies	rsid	Frequencies, clinical significance
gnomad_get_variant	gnomAD metadata	variant_id (CHR-POS-REF-ALT)	Basic variant info
EnsemblVEP_annotate_rsid	Consequence prediction	variant_id (rsID)	Transcript impact

Structural Variant Annotation

Tool	When to Use	Parameters	Response
gnomad_get_sv_by_gene	SV population frequency	gene_symbol	SVs with AF, AC, AN
gnomad_get_sv_by_region	Regional SV search	chrom, start, end	SVs in region
ClinGen_dosage_by_gene	Dosage sensitivity	gene_symbol	HI/TS scores, disease
ClinGen_dosage_region_search	Dosage-sensitive genes in region	chromosome, start, end	All genes with HI/TS scores
ensembl_get_structural_variants	Known SVs from DGVa/dbVar	chrom, start, end, species	Clinical significance

See references/annotation_guide.md for detailed tool usage examples

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Common Use Patterns

# Quick summary
report = variant_analysis_pipeline("input.vcf", output_file="report.md")

# Filtered analysis
report = variant_analysis_pipeline("input.vcf",
    filters=FilterCriteria(min_vaf=0.1, min_depth=20, pass_only=True))

# Annotated report (top 50 variants with ClinVar/gnomAD/CADD)
report = variant_analysis_pipeline("input.vcf", annotate=True, max_annotate=50)

pandas vs python_implementation: Use python_implementation for parsing/classification/annotation, then convert to DataFrame for custom aggregations:

vcf_data = parse_vcf("input.vcf")
passing, _ = filter_variants(vcf_data.variants, criteria)
df = variants_to_dataframe(passing, sample="TUMOR")

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Limitations

• VCF annotation required for mutation classification: If VCF has no ANN/CSQ/FUNCOTATION in INFO, mutation types will be "unknown" until ToolUniverse annotation is applied
• Multi-allelic variants: Parser takes first ALT allele for type classification
• ToolUniverse annotation rate: API-based, limited to ~100 variants per batch by default to respect rate limits
• gnomAD tool: Returns basic metadata only (not full allele frequencies); use MyVariant.info for gnomAD AF
• Large VCFs: Pure Python parser streams line-by-line; cyvcf2 is recommended for files with >100K variants

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Reference Documentation

• references/vcf_filtering.md: Complete filter options and examples
• references/mutation_classification_guide.md: Detailed mutation type classification rules
• references/annotation_guide.md: ToolUniverse annotation workflows with examples
• references/sv_cnv_analysis.md: Complete SV/CNV interpretation workflow

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Additional Resources

• Scripts: scripts/parse_vcf.py, scripts/filter_variants.py, scripts/annotate_variants.py
• Quick start recipes and MCP examples: QUICK_START.md