Missing NaNs in correlation matrix for fine-mapping

Question

[always_learning]

Hi, Does anyone have experience running fine mapping of GWAS hits? I am stuck at the correlation matrix steps. I generated a correlation matrix with few NaNs although I don’t have any missing genotypes. Is that a common problem everyone encounters, and how do we tackle it? Since it has NaN in my matrix, so next fine-mapping steps isn't working.

I tried using Plunk and LDstore2 and am getting the same issues. can some one please help me on this ?

Regards