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- - analyze_covariates.xml - | - -- - | -|
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- - base_recalibrator.xml - | - -- - | -|
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- - combine_gvcfs.xml - | - -- - | -|
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- - combine_variants.xml - | - -- - | -|
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- - gatk.xml - | - -- - | -|
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- - gatk_macros.xml - | - -- - | -|
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- - genotype_gvcfs.xml - | - -- - | -|
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- - haplotype_caller.xml - | - -- - | -|
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- - indel_realigner.xml - | - -- - | -|
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- - print_reads.xml - | - -- - | -|
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- - realigner_target_creator.xml - | - -- - | -|
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- - tool_dependencies.xml - | - -- - | -
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- - - README -
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- 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. -