Table 2 List and description of Nextflow scripts by phase of GWAS

Pre-association

qc/qc.nf

Quality control of genetics data

call2plink/main.nf

Converting from Illumina genotyping reports in TOP/BOTTOM or Forward

Association testing

assoc/main.nf

Run association and GxE using genetics on PLINK file and phenotype(s)

Post-association analysis

finemapping/cojo-assoc.nf

Stepwise model selection procedure to select independently associated SNPs

finemapping/cond-assoc.nf

Run conditional association using gemma

finemapping/finemap_region.nf

Fine-mapping on specific region using FineMap,

finemapping/main.nf

Extract lead SNPs and perform a fine-mapping on each region using FineMap,

heritabilities/main.nf

Estimated heritability using GCTA, BOLT-LMM, LDSC or GEMMA

replication/gwascat/main.nf

Extraction of replication using GWAS catalog by positions and linkage disequilibrium.

meta/meta-assoc.nf

Meta analysis using PLINK, Meta-soft, GWAMA and Metal

meta/mtag-assoc.nf

Multi-trait genome-wide association using mtag software

utils/annotation/annot-assoc.nf

Locus zoom, annotation using , distribution of phenotype by genotype

utils/build_example_data/main.nf

Extracted genotype for a sample and simulated phenotype with GCTA using 1000 Genome and positions, effect of catalog results

utils/build_example_data/simul-assoc_gcta.nf

Simplified version of main.nf, simulated phenotype with GCTA using 1000 Genome and positions, effect of catalog results

utils/build_example_data/simul-assoc_phenosim.nf

Simulated phenotypes using phenosim with random choice of positions and run association on simulated phenotypes

Format data

formatdata/convert_posversiongenome.nf

Convert position between reference

formatdata/format_gwasfile.nf

Format GWAS file

formatdata/plk_in_vcf_imp.nf

Format PLINK in VCF for imputation

formatdata/vcf_in_bimbam.nf

Use VCF output of imputation to format in bimbam

formatdata/vcf_in_impute2.nf

Use VCF output of imputation to format in impute2 format

formatdata/vcf_in_plink.nf

Use VCF output of imputation to format in PLINK format

formatdata/vcf_in_bgen_merge.nf

Use VCF output of imputation to format in bgen format