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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/