Coverage not correct

[parlundin]

Seems like qualimap wrongly use the duplicates when calculating coverage.

[ewels]

Qualimap issues page: https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open

[johandahlberg]

I've submitted a feature request on this now: https://groups.google.com/forum/#!topic/qualimap/xQlXwuJl2r0

[b97pla]

new version still doesn't support excluding only the Picard-marked duplicates, a new feature request has been made: https://bitbucket.org/kokonech/qualimap/issues/26/bam-qc-add-an-option-to-control-skip