Add joint calling as an option to the pipeline

[bhanugandham]

Add joint calling as an option to the variant calling calling pipeline. Some microbial analysis has benefited from the joint calling steps, such as the fungal. Also evaluate the difference with and without the joint calling steps.

[bhanugandham]

This optional wdl can also be used to call variants on core genomes of bacterial species which have conserved regions. It can then be used to evaluate differences between strains wrt to their core genomes.