I am currently doing my project work on Exome sequencing and is using the following tutorial (Exome sequencing data analysis for diagnosing a genetic disease). I have an error in GEMINI load tool. It is showing that the VCF format is unavailable(SNPEff eff). Please look into the problem and help me with it. Thank you
Hi @Thara_Dharanidhar
not quite sure what we are seeing in those screenshots.
Apparently, you’ve run the tool already and have produced a gemini.sqlite dataset with it?
Anyway, the reason why the Vcf dataset is not offered in the select box is likely that you haven’t set a format/dbkey on it. Click on the pencil icon on your dataset and set the dbkey to hg19.
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Hi @wm75
I did exactly what you told but i am not getting the output. I set the dbkey as hg19 but no result.Can u suggest alternative tool instead of GEMINI load.
I’m sorry, but I don’t understand what the issue is. You have obtained a GEMINI load dataset and its state is green. Everything looks good and you can just continue with the tutorial, can’t you?
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Hi@wm75
GEMINI load tool is working and its state is also green but I am unable to view the output as some file is getting downloaded every time I click the view option. What kind of data will be obtained from GEMINI load tool as you can see my screenshot showing that (loading chunk 1 , loading chunk 2…) So the data will look like this or in some other format. Please help me out.
This file is getting downloaded whenever I click the view data . When I click the file this message appears “file cannot be viewed”.
Yes, the GEMINI load tool produces a GEMINI database, which is not intended to be viewed, but queried. Please follow the tutorial, which explains a few ways how you can do that.
These tutorials: Identification of somatic and germline variants from tumor and normal sample pairs and Calling variants in diploid systems demonstrate more options.
Think of the GEMINI database as a computer-friendly version of a VCF. You can’t read it, but queries are very efficient. The GEMINI load tool is essentially the converter that takes VCF and produces the database format.
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Hi@wm75
Thank you so much for your help.