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feat(eqtl): comprehensive eQTL analysis methods, config, and visualization
New modules: - gwas/finemapping/eqtl.py: cis/trans eQTL scan, conditional analysis, effect sizes - gwas/visualization/eqtl_visualization.py: volcano, boxplot, LocusZoom plots New config: - config/eqtl/eqtl_amellifera.yaml: A. mellifera eQTL config linking RNA + GWAS Tests: 17 passing tests for eQTL integration
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‎config/eqtl/README.md‎

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# eQTL Configuration
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Configuration files for expression Quantitative Trait Loci (eQTL) analysis.
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## Files
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| File | Description |
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|------|-------------|
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| `eqtl_amellifera.yaml` | *Apis mellifera* eQTL analysis config |
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## Quick Start
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```bash
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# Run eQTL analysis with config
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uv run python scripts/eqtl/run_eqtl_analysis.py --config config/eqtl/eqtl_amellifera.yaml
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```
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## Configuration Sections
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- **expression**: RNA-seq data paths, normalization settings
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- **variants**: VCF file, MAF filters
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- **annotations**: Gene positions for cis-window
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- **cis_eqtl**: Window size, FDR thresholds
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- **trans_eqtl**: Trans analysis settings (optional)
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- **colocalization**: GWAS integration
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- **output**: Results and plots directories
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## Data Sources
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Requires:
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1. **Expression data**: `output/amalgkit/apis_mellifera_all/work/quant/`
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2. **Variants**: `output/gwas/amellifera/variants/`
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3. **Annotations**: `output/gwas/amellifera/genome/genomic.gff`
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## See Also
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- [config/gwas/](../gwas/) - GWAS configuration
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- [config/amalgkit/](../amalgkit/) - RNA-seq pipeline config

‎config/eqtl/eqtl_amellifera.yaml‎

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# METAINFORMANT eQTL Configuration
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# Species: Apis mellifera (Western Honey Bee)
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# Purpose: Expression QTL analysis linking GWAS variants to RNA expression
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# =============================================================================
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# EXPRESSION DATA
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# =============================================================================
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# RNA-seq expression data from kallisto quantification
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expression:
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# Directory containing sample abundance files
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quant_dir: output/amalgkit/apis_mellifera_all/work/quant/
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# Expression matrix file (if pre-merged)
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# expression_matrix: output/amalgkit/apis_mellifera_all/work/merge/expression_matrix.tsv
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# Gene-level or transcript-level
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level: transcript
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# TPM threshold for expressed genes
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min_tpm: 1.0
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# Minimum samples with expression
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min_samples_expressed: 10
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# Normalization method: tpm, tmm, or quantile
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normalization: tmm
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# =============================================================================
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# VARIANT DATA
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# =============================================================================
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# GWAS variant data for eQTL association
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variants:
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# VCF file with genotype dosages
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vcf_file: output/gwas/amellifera/variants/amellifera_population.vcf
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# Minimum minor allele frequency
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min_maf: 0.05
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# Maximum missing rate
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max_missing: 0.1
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# Variant positions file (if separate from VCF)
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# positions_file: output/gwas/amellifera/variants/variant_positions.tsv
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# =============================================================================
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# GENE ANNOTATIONS
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# =============================================================================
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# Gene/transcript position information for cis-window definition
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annotations:
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# GFF3 or GTF file
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gff_file: output/gwas/amellifera/genome/genomic.gff
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# Gene positions TSV (gene_id, chrom, tss_position)
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# gene_positions: output/gwas/amellifera/annotations/gene_positions.tsv
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# Feature type to extract (gene, mRNA, exon)
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feature_type: gene
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# =============================================================================
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# CIS-eQTL ANALYSIS
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# =============================================================================
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cis_eqtl:
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# Enable cis-eQTL analysis
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enabled: true
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# Window size around TSS (bp)
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window: 1000000 # 1Mb
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# Minimum samples for testing
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min_samples: 30
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# FDR threshold for significance
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fdr_threshold: 0.05
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# Permutation-based significance (slower but more accurate)
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permutations: 0 # 0 = no permutation, 1000 recommended for final analysis
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# =============================================================================
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# TRANS-eQTL ANALYSIS
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# =============================================================================
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trans_eqtl:
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# Enable trans-eQTL analysis
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enabled: false # Computationally expensive
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# P-value threshold for reporting (pre-FDR)
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pvalue_threshold: 1.0e-6
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# FDR threshold for significance
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fdr_threshold: 0.01
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# =============================================================================
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# COLOCALIZATION
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# =============================================================================
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# Colocalization with GWAS phenotype associations
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colocalization:
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enabled: true
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# GWAS summary statistics file
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gwas_sumstats: output/gwas/amellifera/results/varroa_resistance.tsv
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# Colocalization method: coloc or clpp
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method: coloc
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# Posterior probability threshold for shared causal variant (H4)
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pp_h4_threshold: 0.75
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# =============================================================================
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# SAMPLE MATCHING
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# =============================================================================
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# Sample ID mapping between expression and genotype data
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samples:
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# Sample ID mapping file (expression_id, genotype_id)
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# mapping_file: output/eqtl/amellifera/sample_mapping.tsv
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# Covariates to include (population PCs, batch, etc.)
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covariates:
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- PC1
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- PC2
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- PC3
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# Covariate file path
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# covariates_file: output/gwas/amellifera/structure/pca_covariates.tsv
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# =============================================================================
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# OUTPUT
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# =============================================================================
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output:
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# Output directory
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results_dir: output/eqtl/amellifera/results
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# Plots directory
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plots_dir: output/eqtl/amellifera/plots
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# Output format: tsv, json, parquet
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format: tsv
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# Generate summary report
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summary_report: true
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# =============================================================================
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# COMPUTATIONAL
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# =============================================================================
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compute:
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threads: 8
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memory_gb: 16
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# Batch processing for large datasets
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batch_size: 1000 # genes per batch
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# Random seed for reproducibility
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seed: 42

‎output/amalgkit/apis_mellifera_all/work/quant/SRR10030225/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 36298267,
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"n_pseudoaligned": 29365958,
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"n_unique": 12893561,
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"p_pseudoaligned": 80.9,
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"p_unique": 35.5,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:20:13 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR10030225 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR10030225/SRR10030225.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR10030260/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 33933530,
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"n_pseudoaligned": 24992338,
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"n_unique": 9178145,
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"p_pseudoaligned": 73.7,
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"p_unique": 27.0,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 08:51:50 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR10030260 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR10030260/SRR10030260.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR1254943/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 7586964,
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"n_pseudoaligned": 5956799,
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"n_unique": 3611675,
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"p_pseudoaligned": 78.5,
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"p_unique": 47.6,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:17:52 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR1254943 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR1254943/SRR1254943.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR14494818/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 5381117,
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"n_pseudoaligned": 5044398,
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"n_unique": 2990289,
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"p_pseudoaligned": 93.7,
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"p_unique": 55.6,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:22:34 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR14494818 -t 2 /Volumes/blue/data/apis_mellifera/SRR14494818/SRR14494818_1.fastq.gz /Volumes/blue/data/apis_mellifera/SRR14494818/SRR14494818_2.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR26149819/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 9286835,
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"n_pseudoaligned": 5979778,
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"n_unique": 1030023,
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"p_pseudoaligned": 64.4,
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"p_unique": 11.1,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:21:28 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR26149819 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR26149819/SRR26149819.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR26149866/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 8846554,
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"n_pseudoaligned": 4614179,
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"n_unique": 697600,
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"p_pseudoaligned": 52.2,
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"p_unique": 7.9,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:16:56 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR26149866 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR26149866/SRR26149866.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR26150166/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 9181469,
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"n_pseudoaligned": 4045193,
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"n_unique": 624440,
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"p_pseudoaligned": 44.1,
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"p_unique": 6.8,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:22:30 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR26150166 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR26150166/SRR26150166.fastq.gz"
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}

‎output/amalgkit/apis_mellifera_all/work/quant/SRR9705235/run_info.json‎

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{
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"n_targets": 28355,
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"n_bootstraps": 0,
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"n_processed": 16406968,
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"n_pseudoaligned": 12455073,
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"n_unique": 8542421,
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"p_pseudoaligned": 75.9,
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"p_unique": 52.1,
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"kallisto_version": "0.51.1",
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"index_version": 13,
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"k-mer length": 31,
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"start_time": "Thu Feb 5 09:21:46 2026",
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"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR9705235 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR9705235/SRR9705235.fastq.gz"
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}

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