Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Missing a VCFCodec

tguchtguch BostonPosts: 3Member

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.
Thanks!

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Answers

  • tguchtguch BostonPosts: 3Member

    I was actually able to find the VCF files in this path GenomeAnalysisTK-2.6-5\GenomeAnalysisTK-2.6-5-gba531bd\GenomeAnalysisTK\org\broadinstitute\variant\vcf and I changed the path location in the code, but it still can't seem to find or recognize it. Do you happen to know why this is and how to fix it?
    Thanks!

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