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lifebit-ai / gwas

GWAS pipeline using SAIGE
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GEL GWAS

Example usage

nextflow run main.nf \
  --plinkFile "s3://lifebit-featured-datasets/projects/gel/gel-gwas/testdata/sampleA.{bed,bim,fam}" \
  --phenoFile s3://lifebit-featured-datasets/projects/gel/gel-gwas/testdata/sample.phe \
  --phenoCol PHE \
  --vcfsList s3://lifebit-featured-datasets/projects/gel/gel-gwas/testdata/vcfs.csv