I want to know if the major HGVS Consequence on the variant table of a specific gene is also located at the beginning of the VEP field in gnomad.exomes.r2.1.1.sites.vcf.bgz.
In other words, each variant ID has an HGVS Consequence in the variant table. Can I see this HGVS Consequence first in the VEP field of gnomad.exomes.r2.1.1.sites.vcf.bgz?
Also, can I find transcript information below ‘Variant Effect Predictor’ when I click on the variant ID in the VEP field of gnomad.exomes.r2.1.1.sites.vcf.bgz?
The example is from SNV:6-35471593-A-G(GRCh37) (gnomAD v2.1.1)
Hello,
The fields in the VCF could be found in the vcf header, if you look at ##INFO=<ID=vep, you will see all the fields, including “HGVSp”. gnomAD vcf are in v4.2 format, please refer to this specification and relevant tools if you want to work VCF.
@Qin
I think the ordering of transcripts in the ##INFO=<ID=vep> field of the VCF file does not seem to follow the VEP transcript order for each variant as displayed on the gnomAD website. I would like to confirm whether the transcripts in the INFO column of the VCF file are listed in the same order as they appear on the website (with the canonical transcript listed first).
