Hi Carlos,

Thanks for reporting this issue. Most (but not all) of the ROD files for the 
GATK now require VCF. I have updated Indel Realigner in changeset 
6320:945c7a47755f to reflect this.


Thanks for using Galaxy,

Dan


On Nov 21, 2011, at 4:27 PM, Carlos Borroto wrote:

> Hi,
> 
> I found that the ROD file for the 'Unified Genotyper' tool, can be
> only vcf format. However for 'Count Covariates' and 'Indel Realigner',
> it can be vcf o, gatk_dbsnp or bed. Is this a bug or there is a
> limitation on GATK?
> 
> Thanks,
> Carlos
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