v1.14.0 - Adds ability to disable duplicate marking

bwa_mem.pl:

• new option -nomarkdup allows generation of BAMs without running duplicate removal
  • For some types of quantitive targeted/amplicon analysis this is necessary.
• deprecated option -charts - has been non funtional since switch to bam_stats from bam_stats.pl
  • Still possible to generate with bam_stats.pl (if this is imperative to your use case please let us know)

Upgrade

• biobambam2 - 2.0.31