How to plot SNP distribution or coverage using vcf files?

Question

[sorabhsethi4]

Hello,

I want to have SNP distribution plots (vertical lines depicting chromosomes with SNP distribution on them). I have a SNP vcf file with SNPs and chromosomal position (standard vcf file after SNP calling) information. I do not want tables, I want figure showing distribution of SNPs chromosome wise. Do we first need to find LD for this? Please help if anyone knows how to do this.

Thank you

[barslmn]

It's not very clear what you're asking for. Could you doodle the image in your head?

[sorabhsethi4]

I think now you can understand my question in better way. Please let me know if you understand what I am asking. Thank you.

[colindaven]

Do you mean a Manhattan plot commonly performed after GWAS ? https://en.wikipedia.org/wiki/Manhattan_plot

Answer 1

[LauferVA]

There are many software programs that do this, see these google image results, for example.

For that reason one that we will recommend depends on your exact goals. For instance, suppose you want just a few SNPs and you are primarily interested in what chromosome they are on. Then, something like phenogram could work.

But, you may have no interest in this, and instead you want to look at all the SNPs within 100kB of a certain gene - then you want something much more close up. For this perhaps something like gene vista, or the NCBI or Ensembl websites, which now have this functionality built into the browser.

A fairly customizable option that will work over any desired length of DNA segment is UCSC genome browser ... you can load your own data in there (see My Data at the top of the link) or if you do not want to wrestle with loading in your own data, you can select the dbSNP track and look at the SNPs within their genomic context.

If you tell us more exactly what you want, we can provide more specific guidance.