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Selphi Example — Quick Start

Tiny example dataset (chr22:20M-25M, 100 ref samples, 2 target samples) for testing the full pipeline immediately after installation.

Setup

Extract the example data:

cd example
unzip example_data.zip
cd ..

This creates three directories: data/, selphi_ref/, and results/.

Dataset

File Description
data/ref_panel.bcf 100 reference samples, 149K variants (chr22:20M-25M)
data/target.vcf.gz 2 target samples (chip array, 1036 variants)
data/truth.vcf.gz 2 truth samples (WGS, 149K variants)
data/genetic_map.chr22.map PLINK genetic map (chr22, trimmed to region)
selphi_ref/ Pre-built reference panel (ready to use)

Usage

All commands assume you are in the repository root and Selphi is installed (see main README).

1. Imputation (uses pre-built reference)

selphi \
  --target example/data/target.vcf.gz \
  --refpanel example/selphi_ref/chr22 \
  --map example/data/genetic_map.chr22.map \
  --outvcf example/results/imputed \
  --cores 4

Output: example/results/imputed.vcf.gz

2. Rebuild reference panel (optional)

selphi \
  --prepare_reference \
  --ref_source_vcf example/data/ref_panel.bcf \
  --refpanel example/selphi_ref/chr22 \
  --cores 4

Using Docker instead

docker run -v $(pwd)/example:/example selphi \
  --target /example/data/target.vcf.gz \
  --refpanel /example/selphi_ref/chr22 \
  --map /example/data/genetic_map.chr22.map \
  --outvcf /example/results/imputed \
  --cores 4

Expected output

With only 2 samples and 100 reference haplotypes, per-variant accuracy is limited by sample size. This example validates that the full pipeline runs correctly, not production-level accuracy. Imputation should complete in under 15 seconds on a modern machine.