CheckRef

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CheckRefAllele Switch Checker

Detect and correct allele switches between VCF files and reference panels

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🔬

Nextflow Workflow

Scalable and reproducible pipeline built with Nextflow DSL2 for seamless execution across platforms.

🧬

Allele Switch Detection

Automatically identifies REF↔ALT orientation mismatches between target VCF files and reference panels.

✅

VCF Validation

Comprehensive file integrity checks detect corrupted, empty, or malformed VCF files before processing.

🔄

Two Fix Methods

Choose to remove problematic sites or correct allele orientations by swapping REF↔ALT alleles.

🧪

Build Mismatch Detection

Gracefully exits when genome builds don't match (e.g., hg19 vs hg38) to prevent incorrect results.

📊

Comprehensive Reporting

Per-chromosome and aggregated statistics with validation and verification reports.

🐳

Container Support

Run with Docker, Singularity, Podman, Shifter, or Charliecloud for maximum reproducibility.

⚡

Automated Matching

Intelligent chromosome detection automatically pairs VCF files with corresponding legend files.

Quick Start ​

Run the pipeline with minimal configuration:

bash
# Install Nextflow
curl -s https://get.nextflow.io | bash

# Run with test data
nextflow run AfriGen-D/checkref -profile test,docker --outdir results

# Run with your data
nextflow run AfriGen-D/checkref \
    --targetVcfs "sample*.vcf.gz" \
    --referenceDir /path/to/reference/panels/ \
    --fixMethod correct \
    --outdir results \
    -profile docker

Pipeline Overview ​

CheckRef performs seven key steps:

  1. VCF Validation - Assess file integrity and format compliance
  2. Chromosome Detection - Automatically identify chromosomes from filenames
  3. Reference Matching - Pair VCF files with corresponding legend files
  4. Allele Switch Detection - Compare REF/ALT orientations against reference
  5. Correction/Removal - Fix allele switches or remove problematic sites
  6. Verification - Validate that corrections were successful
  7. Results Aggregation - Generate comprehensive summary reports

Use Cases ​

  • Quality Control before genotype imputation
  • Data Harmonization across different reference panels
  • Genomic Data Cleaning for association studies
  • Reference Panel Preparation for population genetics research

Documentation ​

Requirements ​

  • Nextflow ≥ 21.04.0
  • Docker, Singularity, Podman, Shifter, Charliecloud, or Conda
  • Java 11 or later (for Nextflow)

Support ​

About AfriGen-D ​

CheckRef is part of the AfriGen-D project, dedicated to enabling innovation in African genomics research through cutting-edge bioinformatics tools, curated datasets, collaborative networks, and capacity building.

Released under the MIT License.

Copyright © 2025 AfriGen-D Project