search

AshleyLab / risk_scores

LD Pred risk scores for afib
0 stars 0 forks source link

Compare the effect allele of GWAS SS and UKBB AFib Plink files #14

Open jackosullivanoxford opened 5 years ago

jackosullivanoxford commented 5 years ago
  1. In step 1 of LDpred, make sure the effect allele in the GWAS Summary Statistics is being entered appropriately into step 1 ldpred code, e.g. --A1 (ldpred code) = Allele1 (GWAS SS), also make sure it matches the PLINK files (which are used as the LD reference panel)
  2. In step 3 of LDpred, make sure the effect allele (A,T, C, G) are the same between the GWAS Summary statistics and the AFib genotype file.