On 11/29/2012 11:09 PM, Fenglou Mao wrote:

When I use an old version of GATK, it failed with a report "-nt" option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report "-et NO_ET" need a key file to work since new GATK force users to report usage unless we obtain a key file, but it seems no place for galaxy to specify the key file.

We are using GATK 1.4 with success. ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTK-1.4.tar.bz2 Hope this helps, Mauro

Any help?

Thanks, Frank

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-- Mauro