# GEMINI load alternatives

**URL:** <https://help.galaxyproject.org/t/gemini-load-alternatives/264>\
**Category:** usegalaxy.org support\
**Tags:** variant-analysis\
**Created:** [December 19, 2018, 8:14am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264 "2018-12-19T08:14:38Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![hov](https://avatars.discourse-cdn.com/v4/letter/h/f04885/32.png) [@hov](https://help.galaxyproject.org/u/hov)\
**Post date:** [December 19, 2018, 8:14am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/1 "2018-12-19T08:14:39Z")

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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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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [December 19, 2018, 8:26am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/2 "2018-12-19T08:26:25Z")

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

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**Author:** ![hov](https://avatars.discourse-cdn.com/v4/letter/h/f04885/32.png) [@hov](https://help.galaxyproject.org/u/hov)\
**Post date:** [December 19, 2018, 8:41am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/3 "2018-12-19T08:41:58Z")

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I need to find SNPs related to cataract.

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [December 19, 2018, 9:01am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/4 "2018-12-19T09:01:55Z")

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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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**Author:** ![hov](https://avatars.discourse-cdn.com/v4/letter/h/f04885/32.png) [@hov](https://help.galaxyproject.org/u/hov)\
**Post date:** [December 19, 2018, 9:28am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/5 "2018-12-19T09:28:55Z")

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

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [December 19, 2018, 9:57am UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/6 "2018-12-19T09:57:57Z")

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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 [https://usegalaxy.org](https://usegalaxy.org) you can find them combined nicely in the _NGS: VCF Manipulation_ section of the tools, on [https://usegalaxy.eu](https://usegalaxy.eu) they are part of the section _Variant Calling_.

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**Author:** ![hov](https://avatars.discourse-cdn.com/v4/letter/h/f04885/32.png) [@hov](https://help.galaxyproject.org/u/hov)\
**Post date:** [December 21, 2018, 12:48pm UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/7 "2018-12-21T12:48:14Z")

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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?

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<div class="post-metadata">

**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [December 21, 2018, 2:17pm UTC](https://help.galaxyproject.org/t/gemini-load-alternatives/264/8 "2018-12-21T14:17:34Z")

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_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.