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.

error in tutorial

Nick_BeesonNick_Beeson Posts: 20Member

http://www.broadinstitute.org/gatk/guide/topic?name=tutorials
in Step 3, the example of code still has the deprecated walker
-T AnalyzeCovariants
which when used generates this,
"ERROR MESSAGE: Walker AnalyzeCovariates is no longer available in the GATK; it has been deprecated since version 2.0 (use BaseRecalibrator instead; see documentation for usage)"

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