Annotate WGS VCF with Allele Frequencies · Biostar

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Annotate WGS VCF with Allele Frequencies

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

snpeff vcf wgs allele

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updated 1.5 years ago by Pierre Lindenbaum

• written 1.5 years ago by Gabriel •

1 answer

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

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written 1.5 years ago by Pierre Lindenbaum

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