GATK DepthOfCoverage error

usegalaxy.eu support
1

Hi!

I have trouble using the GATK DepthOfCoverage tool.

The following error appears:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:

According to a Google search that could be because of a too old version of java or of GATK.

Is it possible that java or GATK are not up to date? Or is it because I’m doing something wrong? Does GATK works for someone?

Thank you!

Mathias

1 Like
2

Hello,

Many GATK tools currently wrapped for Galaxy are several releases outdated and are considered deprecated. They should not be used.

There is a newer version: https://toolshed.g2.bx.psu.edu/view/lz_hust/gatktools/01ff8dd37d4d

If that new version (released in June 2019) is presenting with problems, please create an issue at the development repository: https://github.com/huster16/gatk-tools

Thanks!

3

Hello,

OK, thank you very much for your explications!

Sincerly,

Mathias

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