Question: (Closed) Where to download a complete Homo sapiens reference genome in gene bank (.gbk) and its.gff annotation to run SNPEff?
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2.4 years ago by
cambridge_hockey0 wrote:

Where to download a complete Homo sapiens reference genome in gene bank (.gbk) and its .gff annotation to run SNPEff on a VCF coming from the Illumina whole genome alignment and variant calling. I have run VEP and wAnnowar on that VCF now want to run SNPEff on it. Could find only genebank .and ,gff3 files of a separate chromosomes.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by cambridge_hockey0

Why not merge the per-chromosome files then?

ADD REPLYlink written 2.4 years ago by Devon Ryan96k

I'd suggest taking a look at the documentation for snpEff here:

http://snpeff.sourceforge.net/SnpEff_manual.html#run

There should be no need to download the .gbk file or the gff3 file. snpEff has pre-built annotation packages for multiple versions of the human genome. However, perhaps I am misunderstanding or there is some special circumstance.

ADD REPLYlink written 2.4 years ago by Sean Davis26k

Hello cambridge_hockey!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink written 2.4 years ago by Michael Dondrup47k
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