Visualize Mutation Frequency
1
1
Entering edit mode
4.8 years ago
justinms ▴ 10

I currently have mutation data for a small patient cohort, for a particular gene, in VCF format. My goal is to visualize the frequency or how many times the variant appears in the gene on the genome browser or IGV without the data being so scattered and would much like to create somewhat of a manhattan plot. Any tips on how to do this?

VCF Mutation Data • 2.0k views
ADD COMMENT
0
Entering edit mode

do You have one VCF per sample ?

ADD REPLY
0
Entering edit mode

No, a VCF with multiple samples

ADD REPLY
0
Entering edit mode

You could submit your variants in VCF format to CRAVAT (http://www.cravat.us/ ). It has an interactive variant viewer.

ADD REPLY
0
Entering edit mode

Wow. This tool is amazing. Love it!

ADD REPLY
0
Entering edit mode

Glad that you liked it.

ADD REPLY
2
0
Entering edit mode

I am actually quite new to bioinformatics. I believe I will have to first familiarize myself with R?

ADD REPLY
0
Entering edit mode

Yes, it's going to be hard to do this without any programming.

Some of these have nice tutorials, so you might be able to follow them if you know some basic R.

ADD REPLY
0
Entering edit mode

Thanks! Will be developing my programming skills as soon as possible

ADD REPLY
0
Entering edit mode

Have you developed them yet?

ADD REPLY

Login before adding your answer.

Traffic: 1635 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6