Using torus to get GWAS PIP: How to determine the prior probability?

[qxliu686]

Hi !
Prof. @xqwen

I am preparing GWAS PIP input using torus .
When I run the example code "torus -d Height.torus.zval.gz --load_zval -dump_pip Height.gwas.pip" ,
I noticed there are 4 columns in the output file "Height.gwas.pip" .
I think the fourth column is the prior probability for a SNP to be causal, but how is this value determined?

Thank you so much for your reply

[xqwen]

It is estimated via the EM algorithm described in the original AOAS paper.