Markov chains from SAM pairwise alignment?

Question

[marc.noguera.julian]

Hi all,

I was wondering if there is any tool that can obtain markov chains from a reference-guided SAM alignment or if that is even conceptually possible?

Thanks
Marc

[dariober]

It's not clear to me what you are trying to achieve. Do you want to shuffle a sequence using a Markov process? Could you give an example of input and expected/desired output?