Add a native GATK implementation for 2bit references, and remove the … #3506

Job	Run time
Validate script WDLs using womtools	1m 38s
build and push gatk docker to artifacts	25m 49s
Validate generated WDLs using womtools	13m 31s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	26m 40s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	26m 37s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	27m 28s
WDL test RUN_M2_WDL on cromwell	20m 37s
WDL test RUN_CNN_WDL on cromwell	21m 26s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	15m 15s
Java 17.0.6+10 build and test cloud	15m 55s
Java 17.0.6+10 build and test integration	33m 3s
Java 17.0.6+10 build and test unit	21m 59s
Java 17.0.6+10 test on docker integration	37m 55s
Java 17.0.6+10 test on docker unit	23m 19s
Java 17.0.6+10 test on docker variantcalling	32m 43s
Java 17.0.6+10 test on docker conda	29m 32s
	6h 13m 28s

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