GEMINI load alternatives

Dear all,

Could you recommend any alternatives to “Gemini load” to work with dog genome (canFam3), since Galaxy “GEMINI load” supports only human genome.

Thanks in advance!

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Well, that depends on what you hope to be able to do. Can you specify?

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I need to find SNPs related to cataract.

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Ok, but how (technically) are you planning to do so. Through studying a pedigree of dogs and following which genes/variants are linked to the phenotype?
What did you hope to get from GEMINI? A report of variants that are inline with some sort of inheritance pattern (recessive/autosomal/…)?

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I would like to filter the HSF4 gene from database and find the pathogenic SNPs.

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Ah I see. Well, for this it sounds as if GEMINI and a database would have been overkill anyway.
Instead, things like that are not too hard to do with the original VCF file:

  • You can use SnpEff to annotate the variants in your VCF with the genes and transcripts affected by them
  • use the SnpSift Filter tool to filter for variants that affect your gene of interest, etc.
  • could have a look at the MiModD Report Variants tool if you find VCF output tedious to parse

Beyond that, there are lots of other tools to manipulate VCF data. On you can find them combined nicely in the NGS: VCF Manipulation section of the tools, on they are part of the section Variant Calling.


Thanks a lot for detailed answer! Anyway, I still have issue since I cannot query my .vcf with gene name or ID, as I understand I need additional file with annotated gene name and ID. Could you give me recommendations?

SnpEff, which I mentioned in my answer above, is the tool you should use to produce a new, annotated VCF with the gene names included.

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