Table 3 List of evaluation of additional workflow implemented in H3AGWAS workflow. using AWI-Gen data set or 1000 genome project
From: H3AGWAS: a portable workflow for genome wide association studies
Script | Test descriptive |
|---|---|
qc/main.nf | QC of genotype 12,000 individuals from AWI-Gen project |
finemapping/main.nf | Extraction of lead SNPs of cholesterol result from GEMMA |
heritabilities/main.nf | Estimation of heritabilities of 4 phenotypes lipid using genotype and phenotype and/or summary statistics |
formatdata/plk_in_vcf_imp | Transformation of PLINK after qc in vcf to prepared data for imputation |
formatdata/vcf_in_plink.nf | Transformation of data imputed in PLINK format |
meta/mtag-assoc.nf | Multi-trait analysis of genome-wide association performed using 4 lipid phenotypes |
utils/build_example_data/main.nf | Build an example data set using diabetes phenotype from lead snps of GWAS catalog and 1000 genomes project genotype [34] |