Entering edit mode
5.2 years ago
misterie
▴
110
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.
Have you tried annovar? Also, you can essentially create/find any ROD file that has
chr,pos,refandaltwith the annotations you need and use it to annotate your VCF usingbcftools annotate.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.
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.
My supervisor told me to do it in snpEff, so I am still looking for solution for snpEff
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 :-)