Update GATK to 4.0.6.0 (requires ReadTools-version in bioinformagik repo)

This update will bring (form 4.0.2.1):

Support to bgzip FASTA references (I am not sure if it would work at the current state) through HTSJDK update
Changes default samjdk.compression_level to 2 (was previously 1)
Added a registry for deprecated/unported tools (this could be useful to add the pre-release names to say that they are not longer supported and to change to 2.0.0)
Smaller artifacts (I hope that also smaller binaries)
New ReadQueryNameComparator (might be useful for us to check sorting order...)

Requires to check the following changes:

~--disable-tool-default-read-filters is now advance argument with a warning message (I guess that we should come back to previous, at least for our tools)~
Updated Picard changes might have some effect

magicDGS / ReadTools