Extract MAF for vcf file

Question

[Sumeet]

Hi All,

I have a vcf file and would like to extract MAF from dbSNP corresponding to each SNP from the vcf file. Doing it one by one would take ages. Any suggestions?

Answer 1

[Pierre Lindenbaum]

convert the dbsnp to CHROM POS REF ALT MAF using bcftools query and then use bcftools annotate to transfert the dbsnp table to your vcf.