I am trying to get the MAF values for the variants in my VCF file in R by biomaRt.
Because the reference file I used to generated the VCF file is HG19. So I cannot use the latest version of the ensembl DB. I checked the Ensembl DB web site and find out the latest version for HG19 (GRCh37) is the archive of Feb 2014(http://useast.ensembl.org/info/website/archives/index.html).
Thus, I connect to this archive in biomaRt and try to get the MAF for my VCF files.
I did the following in R and try to get the MAF for SNP rs200322093:
snpdetail=useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp",host="feb2014.archive.ensembl.org", path="/biomart/martservice",archive=FALSE)
The result I got is NA:
1 NA rs200322093
But I checked dbSNP website, for GRCH37, this snp does have a MAF value, which value is 0.0012.(http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=200322093)
Does anyone know the reason?
In addition, I notice in the latest version of the DB, it has a field called "minor_allele_freq_second", what's the difference between it and MAF?