How to make a skyline plot from ddRAD data

Question

[mesembriomys]

Hi all,

Is it possible to make a skyline plot of demographic history from standard ddRAD data?

I've been told I could perhaps subset down to reads that have > 1 SNP and plug those reads into BEAST. If so, how could I possibly find and retain only reads containing multiple SNPs? The data is currently in .BAM file format.