GATK in Galaxy

[sridhar28]

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

[JackieBadger]

try GATK on it's own.

[sridhar28]

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

[HeidiJTP]

Sridhar,

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