search

wouterpeyrot / CCGWAS

18 stars 6 forks source link

Lacking of frequency of the EA in controls in input GWAS summary data #7

Closed zongchangli closed 2 years ago

zongchangli commented 2 years ago

Hi, I am trying to replicate some of CCGWAS paper findings with PGC GWAS summary datat. I noticed that CC-GWAS requires the FRQ (the frequency of the EA in controls) information in the input data, but for some PGC GWAS summary data(eg. ASD, ASHD), the FRQ information is missing. I want to know that how to address this issue? Thanks

wouterpeyrot commented 2 years ago

In this case, we advice to use the allele frequency in the reference sample that was used for imputation.