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Old 07-28-2013, 08:45 PM   #1
sridhar28
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Location: chennai

Join Date: May 2013
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Default GATK in Galaxy

Dear Users,

I am running GATK (beta ) Unified Genotyper module in galaxy local interface 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 (The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)

Could anybody suggest on the same..

Thanks
Sridhar
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Old 07-28-2013, 08:59 PM   #2
JackieBadger
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try GATK on it's own.
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Old 07-28-2013, 09:07 PM   #3
sridhar28
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hello Jackie,
Thanks for the reply.. i could run GATK in commandline, i am getting results in commanline option but my task is to run it on galaxy.. so i am trying on it..

Could you please suggest on the same..

Thanks
Sridhar
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Old 03-03-2014, 09:02 AM   #4
HeidiJTP
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Sridhar,

Were you ever able to resolve this problem? I am having the same issue.
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