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:)

  • $\begingroup$ Can you paste a snippet of the first few lines of a gnomad file here for us to look at? Generally speaking VCFs can be annotated with genes according to your favorite annotation, here is one of many tools. Alternately, bioinformatics SE might be a better place to get an informative answer. $\endgroup$ Dec 26, 2022 at 6:42
  • $\begingroup$ @MaximilianPress hi it is the regular VCF file for variants that gnomad has on the download page $\endgroup$ Dec 26, 2022 at 7:40
  • $\begingroup$ can you reproduce or link it here so that we don't have to go remember the exact url for that file? $\endgroup$ Dec 26, 2022 at 17:58
  • $\begingroup$ (I'd suggest going and looking at the file header or the first few lines of variants, which directly answer your question) $\endgroup$ Dec 26, 2022 at 18:18
  • $\begingroup$ @MaximilianPress the first lines of the variants are chrom position ref/alternate allele i was wondering if the information is in the INFO column? $\endgroup$ Dec 27, 2022 at 12:08


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