CLASSPATH of GATK version 4.4.0.0 in CFSAN SNP pipeline

Question

[janejin]

I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not configured with the path to GenomeAnalysisTK.jar. I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc file, the classfath setting is: export CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH

I have checked the path and everything is fine in my sense. Can you help me? It is an urgency.

Thank you.

Answer 1

[Pierre Lindenbaum]

There is no such GenomeAnalysisTK.jar in gatk4.*. There is just a executable script gatk that is in charge of running everything.