Question: How to retrieve VCF of C. elegans and D. melanogaster
1
gravatar for Fadel
6 weeks ago by
Fadel20
Malaysia
Fadel20 wrote:

Hi,

As simple as this, I couldn't know how to find VCF variation files of C. elegans nor D. melanogaster.

Since dbSNP does only host human variations, so I tried EVA, but I coudnt find its FTP, and didnt know how to download all variants for those species from Variant Browser

On ensembl, the provided links are not working, C. elegans, D. melanogaster. I tried to email them, but never received any reply.

On FlyBase, WormBase, I couldn't find any VCF files.

I do appreciate any help ..

eva dbsnp ensembl vcf • 218 views
ADD COMMENTlink modified 13 days ago by Emily_Ensembl19k • written 6 weeks ago by Fadel20
2

dbSNP has other organisms (although they are no longer updated): ftp://ftp.ncbi.nih.gov/snp/organisms/archive/

ADD REPLYlink written 6 weeks ago by igor8.3k

thanks igor, this works, but it would be great if we can find a frequently updated source. thanks for your help

ADD REPLYlink written 6 weeks ago by Fadel20

There are species-specific SNP databases, such as BDGP: https://www.fruitfly.org/SNP/

ADD REPLYlink written 6 weeks ago by igor8.3k

I couldnt find any VCF files there. I found FlyVar and be able to download SNPs, INDELs vcf files. This is sub-optimal solution for my case, and I am still hoping to find way to access ensembl or EVA

ADD REPLYlink written 6 weeks ago by Fadel20

I can't see any email in our system from you. Did you email helpdesk or dev? If it was helpdesk, what was your ticket number?

ADD REPLYlink written 13 days ago by Emily_Ensembl19k
3

Ah, I've found it. I see that you emailed us on a Sunday (ie not a work day) and Ben replied to you on Ensembl helpdesk the following day (ie the next working day) and solved your problem, which you acknowledged. I'd rather if you didn't libel us on public fora, if that's OK.

ADD REPLYlink modified 13 days ago • written 13 days ago by Emily_Ensembl19k

I apologize for the late reply, I was away and didn't have an internet connection in the past few days, and I apologize for not updating this thread after I got the reply from Ensembl. That's been said, this is rather a very weird situation, I used Ensembl helpdesk form to report the broken links for more than ten times, using different browsers and machines, but never been able to get the auto-reply email with a ticket number, this is I guess not a surprise since in the helpdesk form itself it says to try again if you didn't receive an auto-reply email within one day !!! So imagine how many days it took me to try more than ten times and none of them worked. Eventually, I gave up and posted my question here since I was in the middle of my simulation study and needed urgent help in that regard. I didn't get a reasonable answer here so I tried to email Ensembl again, but that time I emailed them directly from my Gmail instead of using Ensembl webpage, and It actually worked and got a reply within a day.

I appreciate your reply and all the work is being done by Ensembl, yet: 1. Why the helpdesk system is not reliable? 2. Why you are asking me to not tag Ensembl publically? anyway, it doesn't seem to have any effect since I only got your attention after five weeks!

Thanks

ADD REPLYlink written 9 days ago by Fadel20

OK, will check out the form.

ADD REPLYlink written 9 days ago by Emily_Ensembl19k
3
gravatar for Emily_Ensembl
13 days ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

The question was answered by Ensembl helpdesk the first working day after the ticket was received (despite the OP saying they "never received any reply"). Ben told them:

The D. melanogaster variation database has been discontinued in Ensembl from version 96 onwards.

The Drosophila variation database that was present in Ensembl in release 95 was imported from the DPGP project:
[1] http://jan2019.archive.ensembl.org/info/genome/variation/species/sources_documentation.html#drosophila_melanogaster
[2] http://www.dpgp.org

However, you can still download the the variation data from the release 95 folder of the Ensembl FTP site or the DPGP project pages.

ADD COMMENTlink modified 13 days ago • written 13 days ago by Emily_Ensembl19k
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