Is there tuberculosis whole genome sequencing alignment and variant calling best practice and published protocols?

Question

[flight52612]

Is there tuberculosis whole genome sequencing alignment and variant calling best practice and published protocols? What tools are employed in large institutes like Pasteur`s to align and call variants on tuberculosis WGS short reads? I tried BWA with VarScan and Pilon and NexGene trial, have some clear results, however, need alternative data processing solutions. No native sequences are produced in my city, we use data from public databases. Thank you.