GEMINI load alternatives


#1

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!


#2

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


#3

I need to find SNPs related to cataract.


#4

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/…)?


#5

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


#6

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 https://usegalaxy.org you can find them combined nicely in the NGS: VCF Manipulation section of the tools, on https://usegalaxy.eu they are part of the section Variant Calling.


#7

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?


#8

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.