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generation
tool-data
.shed.yml
README
analyze_covariates.xml
base_recalibrator.xml
combine_gvcfs.xml
combine_variants.xml
gatk.xml
gatk_macros.xml
genotype_gvcfs.xml
haplotype_caller.xml
indel_realigner.xml
print_reads.xml
realigner_target_creator.xml
tool_data_table_conf.xml.sample
tool_dependencies.xml

README

Installation note:
A GATK license needs to be obtained separately from the Broad Institute (https://www.broadinstitute.org/gatk/)
to be able to use this tool. Once the license is obtained, the GATK Jar file must then be downloaded and moved 
to /mnt/galaxy/tools/GATK/x.x-x on the server. Substitute the appropriate version number in the file path. 
Be sure to download the correct version of the Jar file for the toolshed version installed.
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