Question: More general annotation using snpEff
0
gravatar for bwczech
7 months ago by
bwczech70
bwczech70 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 • 330 views
ADD COMMENTlink written 7 months ago by bwczech70

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 7 months ago by RamRS24k

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 7 months ago by bwczech70
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 7 months ago by RamRS24k

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

ADD REPLYlink written 7 months ago by bwczech70
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 7 months ago • written 7 months ago by RamRS24k
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