Identifying CpG islands given a vcf variant file
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6.1 years ago
sagi.polani ▴ 80

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

CpG islands vcf • 2.2k views
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6.1 years ago
  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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Is this relevant also for non-human data?

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

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It seems that the link is broken or incomplete

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5.4 years ago
sagi.polani ▴ 80

Thanks Ryan!

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