Variant Calling between Microbial Populations

Question

[gabriel.jabud]

I was wondering if anyone knew the caveats to doing variant calling on populations of microbes? We have whole genome sequences for several populations that were sequenced. Each population is a single strain. We would like to compare variants across these different populations. They are populations as they weren't streaked and selected for a single colony. The read depth is 200x I believe. Are the standard variant calling tools (such as samtools) sufficient for this case or will that give lots of incorrectly called variants? I have read a couple of articles that say they needed significantly more read depth to account for it being a population, even as high as 18000x (https://www.nature.com/articles/srep45771).