Update GATK to 4.6.0.0 in sv_pipeline_docker

[mwalker174]

Bumps the version of GATK to 4.6.0.0 in sv_pipeline_docker. Note this is not the same as gatk_docker, as gatk is needed in some tasks that use GATK-SV code (e.g. svtk) and so it is built into the sv_base_docker image.

This addresses #81, but also the current commit has rotted with a dependency error, preventing new builds of sv_base_docker.

Note that the newer version of PrintSVEvidence produces an index file with 0-based indexing. This required changing/moving some tabix commands in the WDLs for consistency and to avoid wastefully regenerating the index. The 0-based indexing also caused problems with the sr-count call in GenotypeBatch, since the queries were off by 1 and this is the only place where tabix-based evidence queries require single-base precision.

Tested GenotypeBatch against v0.28.1-beta with the "bwa-melt" test cohort. Discrepancies in the output were minor and could be explained by recent PRs (e.g. #618). Also tested GatherBatchEvidence, GenerateBatchMetrics, ResolveComplexVariants, and GenotypeComplexVariants which passed sanity checks.

[epiercehoffman]

Thanks for unraveling this puzzle! As we discussed offline, it seems that a better long-term solution would be to ensure the index matches the evidence files, but this makes sense as an interim solution to allow the docker to be built with the new GATK version.