Question: More general annotation using snpEff
0
gravatar for misterie
18 months ago by
misterie90
misterie90 wrote:

Hi,

I would like to ask whether is possible to do more general annotation of my VCF files? I mean, snpEff produces annotation like intragenic_variant, splicing_variant, non coding transcript_variant which are not common e.g in VEP. I would like to get more general annotation - UTR, exon, intergenic, intron and so on. I do not know how to handle with e.g. intragenic variant. Can I group it with exon_variant? In VEP everything is more general, but I could not use VEP because of other version of genome, so I have to use snpEff.

snpeff annotation genome • 623 views
ADD COMMENTlink written 18 months ago by misterie90

Have you tried annovar? Also, you can essentially create/find any ROD file that has chr, pos, ref and alt with the annotations you need and use it to annotate your VCF using bcftools annotate.

ADD REPLYlink written 18 months ago by RamRS28k

but the problem is I have to use snpEff and I have problem with some terms such as intragenic_variant, splicing_variant and non coding transcript_variant.

ADD REPLYlink written 18 months ago by misterie90
1

I have to use snpEff

Why? VEP is a much better resource and a lot more up to date as well. If you need VEP-like terms, you're going to have to use VEP or write a mapping between VEP terms and snpEff terms yourself, which most probably is not a 1:1 mapping.

ADD REPLYlink written 18 months ago by RamRS28k

My supervisor told me to do it in snpEff, so I am still looking for solution for snpEff

ADD REPLYlink written 18 months ago by misterie90
1

Just a heads-up: Sometimes, supervisors don't have it 100% right. Try having a discussion with them to explain why you need VEP, once you determine the reason for yourself. I'm sure your supervisor would not disagree with scientific progress :-)

ADD REPLYlink modified 18 months ago • written 18 months ago by RamRS28k
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