Can I use SNPs to date divergence?

Question

[g.frascarelli]

Hi everybody, I have plastome data of different species of common bean and I would like to date their divergence. I called the SNPs to make an NJ tree. Can I use SNPs to create a Nexus file to run BEAST or should I use the entire plastome sequences? Thanks

[jean.elbers]

This is not a BEAST question but rather a SNP/coverage question I pose. Do you have enough sequencing coverage across the targets for all samples to accurately call the consensus on the sequence for each sample that you propose to input as an alignment to BEAST? For example if you have a 1000-bp target, but 100 bases have less than 6x coverage after removing duplicates, then I would say that you could only really call the consensus for the first 900-bp even if you can call a SNP genotype here or there for some samples in the last 100-bp.