Can something like this be done in IGV or other better browsers

Question

[Saad Khan]

Hi

I had generated the following image using ggbio but since it looks too cluttered particularly with respect to the gene structure I was wondering if something like this can be done with IGV or any other browser to make it more publication quality.

http://postimg.org/image/ffzel7n6f/

Regards

[karl.stamm]

What are you trying to show?

[Saad Khan]

I am trying to show single nucleotide variants in a particular gene along with its coverage and reference base at that location

Answer 1

[Dan D]

Everything in that image can be shown in IGV, assuming the reference you load in has the genes data.

The chromosome diagram is shown across the top of the window.

The SNPs would be shown upon loading the VCF

The reference sequence is shown across the bottom of the window, as are the genes and exons if the reference has them available.

A coverage histogram will show automatically after you load a BAM file.

You can always use image-editing software to change the order or proportion of these various segments, but everything in your figure can easily be replicated in IGV.

[thackl]

Dan is right, however, gene models in IGV are even more, well let's say not beautiful.