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Reference dictionary issues

artitandonartitandon Member ✭✭
edited August 2012 in Ask the GATK team

I am running GATK in the UGCalcLikelihoods mode, using a reference sequence made by Heng Li: hs37m.fa. I have indexed this reference and run bwa successfully using it on my sequences and would next like to run GATK on it. When I run GATK with the following command:

"java -jar GenomeAnalysisTK.jar -T UGCalcLikelihoods -R hs37m.fa -L $listfile -out_mode EMIT_ALL_SITES -I $bamfile -o $tempdir/$smpl.$batch.vcf"

I get the following error message:
ERROR MESSAGE: Invalid command line: Failed to load reference dictionary

What can be the issue, and how do I resolve it?


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