Question: Tool to process VCF file
0
gravatar for shuksi1984
9 months ago by
shuksi198450
shuksi198450 wrote:

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.

sequencing next-gen • 406 views
ADD COMMENTlink written 9 months ago by shuksi198450

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.

ADD REPLYlink written 9 months ago by Amitm1.6k
What are you saying? As far as I am aware of, Annovar is free for academic usage
  

I tried to download ANNOVAR from the given link annovar

ADD REPLYlink modified 9 months ago • written 9 months ago by shuksi198450
1

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.

ADD REPLYlink written 9 months ago by ATpoint17k

Yep, it says that its freely available to personal, academic and non-profit use only on 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.

ADD REPLYlink written 9 months ago by Amitm1.6k

Thanks..!! will check with VEP.

ADD REPLYlink written 9 months ago by shuksi198450

I tried to download ANNOVAR from the given link annovar

So you must fall in this category: freely available to personal, academic and non-profit use only. So what was the problem?

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax67k

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.

ADD REPLYlink modified 9 months ago • written 9 months ago by shuksi198450

You should use a *.edu email 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 *.com email address.

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax67k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 935 users visited in the last hour