i tried to run the varscan somatic tool from fcaramia on two pileup files but i got the following error: Unknown Input: COMMAND::java -jar /home/karin/galaxy/dependency_dir/VarScan/2.3.5/fcaramia/varscan/51969e284317/jars/VarScan.v2.3.5.jar somatic
I also tried to change the varscan_somatic.xml file in such a way that i removed the "COMMAND::" tags etc. and used it without the varscan_somatic.pl file. After doing that, the tool ran without errors but i obtained empty files. Redoing the same command on my local computer ran properly and i obtained the wanted outputs:
in dataset_131.dat the snps, indels: dataset_132.dat, and some information (varscan directs this info on stderr) in testlog.
Any idea how to fix that? i appreciate any information on how this may be fixed!
Thanks a lot and best wishes, Karin
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