With HTSJDK >= 1.16.0 (available after #487), I implemented support for bgzip reference sequences. Nevertheless, this is not integrated yet into the Picard/GATK engine. We should either contribute for this support, or request it, as we would like to be able to use it (in their walkers, but also for other parts of the code).
With HTSJDK >= 1.16.0 (available after #487), I implemented support for bgzip reference sequences. Nevertheless, this is not integrated yet into the Picard/GATK engine. We should either contribute for this support, or request it, as we would like to be able to use it (in their walkers, but also for other parts of the code).