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Old 01-15-2012, 11:32 PM   #4
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

The "-R" option is for your reference genome fasta file. This is not to be confused with the refseq ROD for GATK (

I think you will need to generate a sequence dictionary using Picard that has the name

java -jar $PICARD/CreateSequenceDictionary R=~/hg19.fasta O=~/hg19.dict

This may solve it, however later versions of GATK do it on-the-fly.

The help desk at are very responsive.
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