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.
BaseRecalibrator - how do you get the plots to work?
I have used BaseRecalibrator with the -plots option, but no PDF is produced. Is there some other software that is required for this?
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