Hi , Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the genomic location available also: exome/intron..... , if yes then what are the columns that contain this data? is it the INFO column?
thank you:)
1 answer
Yes they do include the VEP annotations in gnomAD as a courtesy. This is not really the point of gnomAD - the allele frequencies are the point. VEP will tell you if something is in an exon, a cds, an intron, etc... It won't really tell you the nearest gene or much at all if it's intergenic. This will all be crammed into a ridiculously hyper-serialized part of the INFO field called vep=
##INFO=<ID=vep,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format:
Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|
CDS_position|Protein_position|Amino_acids|Codons|ALLELE_NUM|DISTANCE|STRAND|VARIANT_CLASS|MINIMISED|
SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|
SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|
LoF|LoF_filter|LoF_flags|LoF_info">
if you have your own VCF then you should annotate it using VEP and --plugin NearestGene
https://uswest.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nearestgene
as you mentioned some variants are not even in gnomAD
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