Recommended Depth of Coverage for Bacterial Genotyping

Question

[michael]

Hello,

Does anyone have a recommendation for the minimum depth of coverage for SNP calling on a bacterial genome? Specifically we are sequencing the tuberculosis genome.

Also, any recommendations about sequencing quality metrics and tools would be much appreciated. We have been using FASTQC to look for contamination and BEDtools genomecov to look at depth of coverage.

Thanks,

Michael