For your version (v.1.48?) of picard-tools try:
If you were to run the command standalone (like below) it will provide you help with all possible options that the command will accept.
The particular version of picard-tools that you installed from Ubuntu repository does not support the reference file option shown by Heisman. This is something you have to get used to and learn. As software develops the developer may add options (or remove some) that were not present in previous versions of the software.
If you want to use the latest version of the software (v. 1.95) you will need to download it from the source here: http://sourceforge.net/projects/picard/files/
Code:
$ picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics
Code:
$ picard-tools CalculateHsMetrics
If you want to use the latest version of the software (v. 1.95) you will need to download it from the source here: http://sourceforge.net/projects/picard/files/
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