Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Running /scripts/genotype+sites.sh example/1000G_MERGED_DEL_2_99615.vcf rundir

An error occurred that I do not understand.

`INFO 15:13:07,421 QScriptManager - Compiling 2 QScripts
INFO 15:13:10,852 QScriptManager - Compilation complete

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.commandline.InvalidArgumentException:
Argument with name 'inputFileIndexCache' isn't defined.
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:307)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:280)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:225)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Argument with name 'inputFileIndexCache' isn't defined.
ERROR ------------------------------------------------------------------------------------------

INFO 15:13:10,901 QCommandLine - Shutting down jobs. Please wait... `

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