GWAS

Univariate GWAS

For univariate GWAS we employed plink2.

Binary trait

plink2 \
  --threads 6 \
  --out out/gwas_sumstats \
  --keep indivs2keep.txt \
  --pfile imputed/pgen.files/genotype \
  --pheno phenotypes.binary.tsv \
  --chr 1-22,X \
  --covar covariates.tsv \
  --covar-variance-standardize \
  --glm firth-fallback hide-covar omit-ref no-x-sex

Continuous trait

  --threads 6 \
  --out out/gwas_sumstats \
  --keep indivs2keep.txt \
  --pfile imputed/pgen.files/genotype \
  --pheno phenotypes.quantitative.tsv \
  --pheno-name cbcl_externalizing,cbcl_internalizing,liability_Xception_without_cbcl,liability_Xception_with_CBCL,liability_Xception_without_cbcl_v2,liability_Xception_with_CBCL_v2,XGB_without_cbcl,XGB_with_cbcl,XGB_without_cbcl_v2,XGB_with_cbcl_v2 \
  --chr 1-22,X \
  --covar covariates.tsv \
  --covar-variance-standardize \
  --glm hide-covar omit-ref no-x-sex

Multivariate GWAS

For multivariate GWAS we employed mvgwas-nf.

nextflow run mvgwas.nf --l 1000 --geno all.chr.vcf.gz --pheno phenotypes.tsv --cov covariates.tsv --out mvgwas.tsv -resume -with-singularity -with-trace -bg -with-mpi

For all other code requests please email [email protected]