Dear Developers,

I am GATK (beta ) Unified Genotyper module to get the indels and SNP.

I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i link the reference genome in .loc file (gatk_sorted_picard_index.loc). I could see the Name i mentioned in the .loc file is appearing in the galaxy page while choosing the Reference genome.

Now while running GATK in galaxy , The command runs for a while and gives ERROR as i am getting ERROR as (The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)

Could anybody suggest on the same..

Thanks
Sridhar