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Is there anyway to generate a jar file to execute a single walker that I wrote?
We have some instructions in this document: http://www.broadinstitute.org/gatk/guide/article?id=1301
but it may be a little out of date. I'll ask @droazen (our build engineer extraordinaire) if he can pitch in with more specific advice.
FYI we are switching the GATK's build system over to Maven, which will make it a lot easier to do what you want. This will be available starting with the next release, which should be just a couple of weeks away now.
Geraldine Van der Auwera, PhD
I've try reading this article, but I got a little confuse. Specially in my case that use GATK as external library for my development. But any help is valid.