Annotate WGS VCF with Allele Frequencies

Question

[Gabriel]

Hi, I'm annotating a whole genome sequence VCF file for the first time. I've had success using SnpEff and SnpSift but the annotations do not include allele frequencies. Allele frequencies seem important for interpretation but I'm having a hard time figuring out how to add these to my VCFs. I'd be happy to get them from any reasonable source (gnomad etc). Can someone please point me towards the right resource for this and how to annotate using SnpEFF or ANNOVAR or similar?

Thanks

Answer 1

[Pierre Lindenbaum]

see SnpSift: Annotate vcf file using GNOMAD "SnpSift: Annotate vcf file using GNOMAD"

or, if you just want the internal AF (in YOUR vcf, not in the gnomad pop)

bcftools +fill-tags in.vcf -- -t AF