added remaing steps to variant calling pipeline. added headers for each step. added a check for the files need for the current step as well as the output file.
added remaing steps to variant calling pipeline. added headers for each step. added a check for the files need for the current step as well as the output file.

emilliman5/Bpipes,emilliman5/Bpipes,emilliman5/Bpipes,emilliman5/Bpipes