Dear experts,

I was wondering whether there are any packages available to automatically run conditional analysis, meaning association of a trait and variants in a region (y ~ SNPs), conditional on the best variant from the primary analysis (y ~ SNPs + top SNP). If there are not, I will proceed from scratch, but if there is any R package or other software to do this automatically from a phenotype and a dosage file with genotypes, vcf or Plink or other any other formats, that would be fantastic! Thank you