Input data for fsc

[Shailesh Kumar Dhudabhai Desai]

Dear Dr. Laurent and fsc community, 

I am bit new to fsc and after browsing the google group, i have some query if anyone can help !

My goal is to estimate various parameter like split and population size, and i have mutation rate.

i have two type of data, type 1 is having ony snp sites, and second data is whole genome, 

I understand that using only snp data without prior, i can not estimate split time, as there is no accurate monomorphic sites in data, and hence i have to use -0, to ignore monomorphic sites, which also by default ignore mutation rate. 

in second data, i have everything, but as fsc assume sites are unlinked, and if do pruning of data (remove high LD sites), then i might lose many SNps and monomorphic sites, so how to deal in this, i am confused. 

i am using eastSFS to compute the SFS data. 

I look forward for any help. 

Many thanks in advance.