Exome sequencing tutorial issue with GEMINI

usegalaxy.org.au support
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1

Once I get to the step using the GEMINI load tool I am unable to continue as the output of the SNPEff eff step is unavailable. Help please!

Thanks,
Sarah

2

Dear @Sarah_Harvey,
We cannot clearly say what went wrong with your data analysis. Can you please either make an error report, or post the error message here, or share your history. Than we can help you better.

Have a nice day and best wishes,
Florian

3

Hello!
One of my students has experienced something similar. We are following the Exome-seq tutorial (Exome sequencing data analysis for diagnosing a genetic disease) and this student could not proceed with the GEMINI LOAD step:

Creating a GEMINI database from a variants dataset

  1. GEMINI load tool with
  • param-file “VCF dataset to be loaded in the GEMINI database” : the output of SnpEff eff etc.

As “his” GEMINI LOAD could not load the vcf_bgzip file (see picture attached)

Galaxy
Galaxy1325×658 77.5 KB

Any hint on what could be happening?
Thanks a lot.
Best,
Marta

4

Welcome, @Marta_Vila!
Can you check the datatype of dataset 40? Also, can you show us the Output format parameter used to generate it?