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Old 08-02-2013, 07:04 AM   #1
jgibbons1
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Location: Worcester, MA

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Default VCF coodinates to Genomic Features from GFF

I think this is a relatively simple question but I haven't been able to figure out a solution yet.

Basically, I have a VCF file of variants and a GFF file of the genome with genomic features. I would like to extract the genomic features (introns, exons, etc.) of each of the variants in the VCF file.

Is there a simple way to glean this information?
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Old 08-02-2013, 07:31 AM   #2
dpryan
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Have you tried using snpEff? I imagine that it can do most of what you want.
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Old 08-02-2013, 07:42 AM   #3
jgibbons1
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Hmmm...have not seen snpEff before but it looks promising.

Thanks for the pointer. I will give this a try.

Any other solutions?
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