# HG changeset patch # User lz_hust # Date 1559387007 14400 # Node ID a4e5c90cf6cb50ec8f36be10cca3ddaa259f3ca8 # Parent e0a6b2ba8bd37ccddb089d18281403539f1484e4 Uploaded diff -r e0a6b2ba8bd3 -r a4e5c90cf6cb gatk-tools --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk-tools Sat Jun 01 07:03:27 2019 -0400 @@ -0,0 +1,1188 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GitHub - huster16/gatk-tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + generation + + + + + +
+ + + + tool-data + + + + + +
+ + + + .shed.yml + + + + + +
+ + + + LICENSE + + + + + +
+ + + + 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 + + + + + +
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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.
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