Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: How to classify the variants into different groups?
0
gravatar for mohamed_refaat.1992
3.4 years ago by
mohamed_refaat.1992 • 10
Egypt
mohamed_refaat.1992 • 10 wrote:

Hello,
This is my first time using galaxy. I ran Free Bayes to detect the variants of a data set against the reference genome, but can't classify the kinds of variants I got according to it's types(snp,mnp,ins,..). 
So i'm asking if there is a tool that can help me detect the number of each variant in my VCF.
Thanks in advance.
vcf • 1.0k views
ADD COMMENT • link •
modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by mohamed_refaat.1992 • 10
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

See the tools in the group "VCF Manipulation" and "NGS: Variant Analysis". The tool "VCFfixup" may be what you want just to gather counts (from say, Freebayes), but there are many other functions available: compare to reference annotations, etc.

If you use Mileup or Naive Variant Caller instead, there are other tool options. See the tool forms to understand which accept these specific input formats.

Additional tools for use in a local/cloud can also be found in the Tool Shed. Just search by "vcf" to bring up the full list of options. 3rd party documentation will help you to understand what each does.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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: 165 users visited in the last hour