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

2. 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

3. 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