Update GATK to v4.6.0.0

[sorelfitzgibbon]

Unless we are adding germline resources with split multiallelics, this update is probably not needed.

Highlights of the 4.6.0.0 release:

• We've fixed a serious CRAM writing bug that affects GATK versions 4.3 through 4.5 and Picard versions 2.27.3 through 3.1.1. This bug can, in limited cases, lead to reads with an incorrect base sequence being written. See https://urldefense.com/v3/__https://github.com/broadinstitute/gatk/issues/8768*issuecomment-2198315437__;Iw!!F9wkZZsI-LA!Gv5X5lVB5qDfXFrbum5AwHSSESbNIhprMyy0IBWZxYHRwS9h7dLBoq6iclR-vPG63D9t_DJfYFJ0DEoWvYtznWzbMHCar5jGHA$ and the full release notes below for more details on what conditions trigger the bug.

       - To help users detect whether their CRAM files are affected, we've released a CRAM scanning tool called CRAMIssue8768Detector that can detect whether a particular CRAM file is affected by this bug. If you suspect that some of your CRAM files may have been affected, please run this tool on them for confirmation!
  

• By overwhelming popular demand, we've switched back to using the standard ./. representation for no-calls in GenotypeGVCFs and GenomicsDB instead of 0/0 with DP=0. This reverts the change described in our article GenotypeGVCFs and the death of the dot.

• We intend to publish a new article shortly to replace that older article with further details on this change. When we do so, we'll link to it from here.

• The Mutect2 germline resource can now have split multiallelic format

• Added an --inverted-read-filter argument to allow for selecting reads that fail read filters from the command line easily

• We've fixed a number of issues with HTTP support, mainly affecting the loading of side inputs such as indices over HTTP

• Reduced the number of layers in the GATK docker image to help users running into docker quota issues