example vtf files aligning sequence data from illumina2bam through bwa mem alignment to production of final bam and cram files. Bamcheck and flagstats, no spatial filtering.
corrected repeated subst_param names which were causing failure to output cram, bamcheck and flagstat files correctly for both target and phix
Merge pull request #24 from dozy/bwa_mem_example

Bwa mem example
Confirming my own pull request - but these are all new files, and they are only examples