The Make Dataset Workflow

This workflow extracts an aggregated dataset containing traits (TRAITS_DATASET), genetic confounders (NB_PCS) and genetic variants (VARIANTS_LIST) in an Arrow tabular format.

Make Dataset

Example Run Command

nextflow run https://github.com/TARGENE/targene-pipeline/ -r TAG -entry MAKE_DATASET -profile P -resume

List Of Workflow Arguments

  • VARIANTS_LIST (required): A text file (one rsid per line) specifying the variants of interest.
  • BGEN_FILES (required): Path to imputed BGEN files from which the variants in VARIANTS_LIST will be extracted.
  • NB_PCS (optional, default: 6): The number of PCA components to extract.
  • BED_FILES (required): Path expression to PLINK BED files.
  • COHORT (optional: "UKB"): Current default for this is UKB. If set to a value other than UKB, this will not run UKB-specific trait extraction.
  • TRAITS_DATASET (required): Path to a traits dataset. If you are running this for a non-UKB cohort, your sample IDs must be specified in the first column of this CSV file, with the column name SAMPLE_ID.
  • FLASHPCA_EXCLUSION_REGIONS (optional, default: assets/exclusionregionshg19.txt): A path to the flashpca special exclusion regions.
  • MAF_THRESHOLD (optional, default: 0.01): Only variants with that minor allele frequency are considered
  • LD_BLOCKS (optional): A path to pre-identified linkage disequlibrium blocks to be removed from the BED files. It is good practice to specify LD_BLOCKS, as it will remove SNPs correlated with your variants-of-interest before running PCA.

If the COHORT argument is set to UKB:

  • UKB_CONFIG (required): YAML configuration file describing which traits should be extracted and how the population should be subsetted.
  • UKB_ENCODING_FILE (optional): If the TRAITS_DATASET is encrypted, an encoding file must be provided.
  • UKB_WITHDRAWAL_LIST (optional): List of participants withdrawn from the study.
  • QC_FILE (optional): Genotyping quality control file from the UK-Biobank study.