Question: How to separate SNPs from other variant types in Galaxy?
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gravatar for vladimir.gritsenko
2.7 years ago by
Tel Aviv University
vladimir.gritsenko90 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 • 765 views
ADD COMMENTlink modified 2.7 years ago by Bjoern Gruening5.0k • written 2.7 years ago by vladimir.gritsenko90
0
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k 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 COMMENTlink written 2.7 years ago by Bjoern Gruening5.0k

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 REPLYlink written 2.7 years ago by vladimir.gritsenko90

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

Anything else you need?

ADD REPLYlink written 2.7 years ago by Bjoern Gruening5.0k

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 REPLYlink written 2.6 years ago by vladimir.gritsenko90

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 REPLYlink written 2.6 years ago by Bjoern Gruening5.0k
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