Merge - Warning

[pawanchk]

Hi Caveman Team,

I am using Caveman version 1.15.1. When I run the third step merge it generates the required output files covs_arr and probs_arr, however I am getting some WARNING messages like these below -

WARNING: At a covariate location where ref base != called base a probability 2.8e-01 higher than the default 2.5e-01 was detected.
This is likely to cause erroneous genotype calls and may be a symptom of some form of incorrect quality manipulation.
WARNING: At a covariate location where ref base != called base a probability 2.7e-01 higher than the default 2.5e-01 was detected.
This is likely to cause erroneous genotype calls and may be a symptom of some form of incorrect quality manipulation.

Since the .covs files and the covs_arr and probs_arr are all binary files, I am not able to find which regions are exactly causing the WARNING messages.

Can I please know how to overcome these WARNING messages ? Please let me know if you require any other details to find the exact issue. I look forward to hearing from you.