HP removes chr from string if present...

... Since we use the 1kg projects reference, and Agilent used hg19 this conversion is necessary to match the files.
HP replaced chrM with MT for hg19->1gkb37 comp
Merge branch 'prepareForMilou' of github.com:johandahlberg/piper into prepareForMilou
Making the conversion optional (default: true)