Missing frequency from GWAS
Opened this issue · 1 comments
ariadnacilleros commented
Hi,
We are currently running a partitioned heritability analysis with our annotation and 10 GWAS. Some of them don't include the frequency of the SNP, and even though I have observed that this information is not among the essential columns required from a GWAS, we would like to know whether including it or not could impact our results.
Thank you so much for this package and the detailed Wiki.
Best,
Ariadna Cilleros
aksarkar commented
@ariadnacilleros No, ldsc does not use the MAF information in the GWAS, only MAF information derived from the reference panel used to estimate LD scores.