ARRAN (Automatic and Reproducible Rare variants and gwas Analyses in Nextflow) is a Nextflow pipeline designed to perform Genome Wide Association Studies (GWAS) and Rare Variants Association Tests (RVAT).
This pipeline uses Plink to perform QC steps and SAIGE/XWAS to perform the association tests. It includes:
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GWAS and Rare Variants Association Tests for Binary or Continuous traits
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Inclusion of chrX (QC specific steps and stratified association tests)
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Generation of logs and plots for the different steps of the pipeline (PCA, Manhattan, QQplot...)
Please refer to our wiki for detailed information about installing, running and interpreting the output of ARRAN.nf.
