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gwas-terra-workflow

Genome-Wide Association Study (GWAS)

Required files:

  • PLINK binary files (.bim, .bed, .fam)
  • list of samples to use (samples.tsv)
  • covariates file (columns: IID, trait, covariates)
  1. recode_plink_split_vcf.wdl

input:

  • basename of PLINK files \
  • PLINK binary files \

output: per chromosome VCF and index files \

Download VCF (.vcf.gz) and Index (.vcf.gz.csi) files from samples table

  1. Upload VCFs to TOPMed and submit for QC, phasing and imputation.

download_unzip_topmed.wdl

input: link and password for download all files from TOPMed \

output: per chromosome VCF and index files

  1. SAIGE_association_testing.wdl

inputs:

  • VCF , Index files and chromosome number (from samples table)
  • trait type: "quantitative" or "binary"
  • covariates file
  • genotype: "GT" or "DS"
  • ID column name
  • phenotype column name
  • covariate column name(s)
  • file with list of samples
  • PLINK binary files \

output: summary statistics from the association tests saved in the samples table

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