How to calculate per site transition probability between hidden states.

Question

[taniamahmood38]

Dear all,

I am running Pool-HMM tool on my pool-seq pileup data. In it, there is an argument

-k (or --k) value, where value is the per site transition probability between hidden states.

My question is what value to give in this argument since I dont know the per site transition probability between hidden states of my data. How can I come to know that? Is there anyway to calculate it? Any help would be highly appreciated.

Thanks in advance