GWAS & Population Genetics

Population QC, ancestry PCA, and GWAS using containerized PLINK2 pipelines.

Category: Genomics Engine: Docker driver Outputs: out/artifacts.json

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Genotype prefix (PLINK2)

Provide the prefix (without extension). Requires .pgen/.pvar(.zst)/.psam.

Phenotype table (TSV/CSV)

Header must start with IID/FID (PLINK2 requirement when using --pheno-name).

Sample ID column

Phenotype column

Phenotype type

Covariates (comma-separated)

Example: age,sex,PC1,PC2. Leave blank for unadjusted GWAS.

mind

geno

maf

hwe

PCA k

Model

Use logistic for binary phenotypes; linear for quantitative traits.

Threads

Run QC Run PCA Run GWAS

This page assumes you mount inputs inside the driver as /in/genotypes and /in/pheno.tsv. Later we can add uploads / dataset-picker integration.