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

Join Date: Apr 2008
Posts: 249
Default

The "-R" option is for your reference genome fasta file. This is not to be confused with the refseq ROD for GATK (http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq)

I think you will need to generate a sequence dictionary using Picard that has the name
~/hg19.dict.

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 http://getsatisfaction.com/gsa are very responsive.
zee is offline   Reply With Quote