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Identifying CpG islands given a vcf variant file

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

vcf cpg-islands
• 4,370 views • link
updated by Ram Ram • written by sagi.polani sagi.polani

2 answers

  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.

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written by Devon Ryan Devon Ryan

Is this relevant also for non-human data?

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written by sagi.polani sagi.polani

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.

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written by Devon Ryan Devon Ryan

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

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written by sagi.polani sagi.polani

Thanks Ryan!

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written by sagi.polani sagi.polani

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