Visualize Mutation Frequency

Question

[justinms]

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?

[Pierre Lindenbaum]

do You have one VCF per sample ?

[justinms]

No, a VCF with multiple samples

[Collin]

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

[justinms]

Wow. This tool is amazing. Love it!

[Collin]

Glad that you liked it.

Answer 1

[igor]

Some R packages that I think might be helpful:

• chromPlot: https://www.bioconductor.org/packages/release/bioc/html/chromPlot.html
• karyoploteR: https://github.com/bernatgel/karyoploteR
• qqman: https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html
• ggbio: http://www.tengfei.name/ggbio/docs/man/layout_karyogram-method.html

[justinms]

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

[igor]

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.

[justinms]

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

[Kevin Blighe]

Have you developed them yet?