Overview Of Vcf Calls Using Artemis??

Question

[Maddox]

Hi,

First time here. I'm immersed for the first time in NGS data. I have generated a small handful of VCF files documenting between ~600 and ~20 000 differences relative to a bacterial reference genome.

I'd like to gain a top-level view of these variants, preferably with a graphic (a picture being worth a 1000 ... etc). So I though Artemis, and specifically DNAplotter, would be ideal.

Is this do-able?

best

m

Hoping not to have to look v-by-v through the sequences in Artemis ....

Answer 1

[Pierre Lindenbaum]

I've just launched the Webstart application for Artemis: http://www.sanger.ac.uk/resources/software/artemis/ , under the "File Menu" there is a menu "Read BAM/VCF files"...

[Maddox]

There is indeed, thanks Pierre. This allows the vcf to be loaded. And then browsed against a reference genome .... all very well; browsing through the 64 variations of one sample is an option, but doing so with the 19257 variations another has is not - hence my query about whether these can be depicted graphically using DNAplotter.

[Pierre Lindenbaum]

OK, my fault, i didn't fully understand your question.

Answer 2

[Rlong]

A seriously top-level view can be had from a circos plot. You have the contigs listed along the circumference, with various tracks of data, copy number, snvs, indels, genes, etc, along the circle.