Tool to process VCF file
I want to annotate the varianst in VCF. Kindly suggest any freely available tool. I have already tried ANNOVAR, but I need to purchase it.
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lincoln.harris •
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shuksi1984 •
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shuksi1984 •
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I'm not totally sure what you mean by 'annotate' but if you're looking to convert genomic variants to peptide-level variants, you can use our tool, cerebra:
https://github.com/czbiohub/cerebra
Freely available on github/pypi, ample documentation.
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What are you saying? As far as I am aware of, Annovar is free for academic usage. There are other tools of course - 1) VEP 2) SNPEff 3) dbNSFP
The last one is more of a database, which can be used with SNPEff or VEP. I am assuming that the variants are from human genome. If so, and if the number of variants is not large, you can use the online VEP referenced above. Else, you can install your local instance of VEP, or SNPEff.
I tried to download ANNOVAR from the given link annovar
I recommend VEP. Even though Annovar's developer makes an outstanding efford to keep it maintained, the base behind VEP is simply larger, and the help desk is fast and helpful in case of problems.
Yep, it says that its
freely available to personal, academic and non-profit use onlyon top of the page.Apologies if that doesn't fit your situation. I am not aware specifically of a variant anno. tool that is free for non-academic/ for-profit use as well. I use VEP. A quick check on their installation/ download page didn't show me of such restrictions as Annovar. You may check their doc. in more detail.
Thanks..!! will check with VEP.
So you must fall in this category:
freely available to personal, academic and non-profit use only. So what was the problem?This is what I got when I tried to download
ANNOVAR is freely available only to personal, academic and non-profit use only.
Because you entered a .com/.co email address, you are required to purchase a license to ANNOVAR from BIOBASE. A BIOBASE representative will contact you to provide you with additional information. In the meantime click here to request a quote for a commercial license or click here for more information. You can also contact info@biobase-international.com directly for commercial license related issues or questions.
You should use a
*.eduemail address, if you have one. This is common domain ending for all academic institutions in US (and perhaps elsewhere). If your academic email address is from a different country (where there is an additional country specific extension after.edu) part then I am not sure what will happen. In any case, I suggest you try using a non*.comemail address.