Identifying CpG islands given a vcf variant file

Question

[sagi.polani]

Hi all,

I'm looking to find a way to identify CpG islands around a given set of variants listed in a vcf file. Any ideas?

Thanks!

Sagi

Answer 1

[Devon Ryan]

1. Download a BED file of CpG islands from UCSC.
2. Use bedtools closest to find the nearest CpG island.

You could also use GenomicFeatures in R.

[sagi.polani]

Is this relevant also for non-human data?

[Devon Ryan]

It's for any species with CpG islands available from UCSC. If there are no such annotation tracks for your organism, you'll need to generate them.

[sagi.polani]

OK, so now I know that such a track does not exist for my organism. How do I continue from here?

[Devon Ryan]

Have a look at this package from Rafael Irizarry's group.

[Antonio R. Franco]

It seems that the link is broken or incomplete

Answer 2

[sagi.polani]

Thanks Ryan!