Document running the tools and any bwa mem options

[nh13]

Requirements:

• run bwa mem:
  • without the -M option (-M marks shorter split hits as secondary).
  • use the -Y option (use soft clipping for supplementary alignments).

Run:

• fgsv SvPileup -i <input.bam> -o <out-pre>.raw
• fgsv AggregateSvPileup -i <out-pre>.raw.txt -o <out_pre>.final.txt