Conditional analysis

In addition to fine-mapping, a more robust way is to use stepwise forward selection (also called iterative conditioning, or conditional analysis) to build iteratively a joint model for a small subset S of SNPs by choosing one SNP at a time to be included in S.This approach was made popular by GCTA’s Conditional & joint (COJO) analysis of GWAS results. The algorithm works as follows:

initially S is empty
repeat until all P-values outside S are > threshold
  add SNP with the lowest P-value to S
  update P-values of all SNPs 'l' outside S using joint model Y ~ X.S + X.l
end repeat