I 'm looking to find a way to identify CpG islands around a given set of variants listed in a vcf file. Any ideas?
You could also use GenomicFeatures in R.
Is this relevant also for non-human data?
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.
OK, so now I know that such a track does not exist for my organism. How do I continue from here?
Have a look at this package from Rafael Irizarry's group.
It seems that the link is broken or incomplete
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