How to generate RefSeq ROD
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Dear team,

I would like to include a RefSeq ROD file in order to get the coverage per gene using the GATK coverage tool (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html). However, it is not really clear to me how I can easily generate such a file, since I can not find the right documentation. All the links that should point to this information seem to be (incorrectly?) redirected to the main GATK homepage). For example this http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html has a link that points to http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq which is redirected to http://www.broadinstitute.org/gatk/. Can someone point me to the correct docs? Other resources I found also point to the same wiki, which I can't find at the moment..

Kind regards, JJ


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