Random extration of reads- how many times should it be done?

Question

[yunnogal]

Hi everyone!

I want to ask you a question. I have nine samples and went through exome sequencing. What I want to do is, I want to mix the nine samples and make a virtual genome, then do phylogenetic analysis. I was advised to randomly select the reads from BAM files and make the phylogeny. But, here is the question.

Would it be good to perform the random selection and make the tree only once? Should I perform the randome selection several times? if yes, how many times? OR, is there any other way to make the random selection and make a phylogeny? Please, I need a big help!

Thank you all!