This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Visualize Mutation Frequency

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
• 3,979 views • link
updated by igor igor • written by justinms • justinms

No, a VCF with multiple samples

• 0 views • link
written by justinms • justinms

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

• 0 views • link
written by Collin Collin

Wow. This tool is amazing. Love it!

• 0 views • link
written by justinms • justinms

Glad that you liked it.

• 0 views • link
written by Collin Collin

1 answer

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

• 0 views • link
written by justinms • justinms

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.

• 0 views • link
written by igor igor

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

• 0 views • link
written by justinms • justinms

Have you developed them yet?

• 1 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this