Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: How to separate SNPs from other variant types in Galaxy?
0
gravatar for vladimir.gritsenko
3.2 years ago by
vladimir.gritsenko • 90
Tel Aviv University
vladimir.gritsenko • 90 wrote:

I have a VCF file with all the called variants. I want to keep just the SNPs. This is achievable in all sorts of ways outside of Galaxy, but I'm curious if (and how) this can be done within Galaxy.

Thanks!

 
vcf galaxy • 925 views
ADD COMMENT • link •
modified 3.2 years ago by Bjoern Gruening ♦ 5.1k • written 3.2 years ago by vladimir.gritsenko • 90
0
gravatar for Bjoern Gruening
3.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:
You can probably use all the ways you are used to from outside of Galaxy from within Galaxy. For example you can annotate your file with snpeff and filter your annotations afterwards. Hope this helps, Bjoern
ADD COMMENT • link written 3.2 years ago by Bjoern Gruening ♦ 5.1k

There is SnpSift varType, but it gives an error (it seems Galaxy only allows access to the "filter" tool from SnpSift). As for "all the ways", well, most tools don't exist in Galaxy (e.g., vcftools - Galaxy uses vcflib instead, which doesn't have that functionality, AFAIK).

ADD REPLY • link written 3.2 years ago by vladimir.gritsenko • 90

VCFtools: https://toolshed.g2.bx.psu.edu/view/devteam/all_vcftools

Anything else you need?

ADD REPLY • link written 3.2 years ago by Bjoern Gruening ♦ 5.1k

That's pretty cool, I didn't know about the Tool Shed. Unfortunately, I need this in the "public" Galaxy (I'm OK with the command line tools, but I do want to find something more user-friendly for the other labmates). Though maybe it's worth it to have our own installation, with all the extra tools.

ADD REPLY • link written 3.2 years ago by vladimir.gritsenko • 90

The Galaxy community makes hosting and running an own Galaxy instance really easy. Especially with Galaxy Docker flavours  the ansible playbooks or VMs with Galaxy. Also consider using CloundMan, a Cloud Galaxy instance for Amazon.

 

ADD REPLY • link written 3.2 years ago by Bjoern Gruening ♦ 5.1k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour