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I've been trying to follow this tutorial in Clojure http://bcbio.wordpress.com/2012/03/04/extending-the-gatk-for-custom-variant-comparisons-using-clojure/ specifically the section under Custom GATK Annotation. I keep getting the error that the org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine is missing. I looked in the jar and there is no VCF folder under the codecs folder. Where can I find the VCF classfile so I can add it?
Sidenote, if anyone else is familiar with this I'd appreciate any help.