Where to download the MAF database from 1000 genomes? ANNOVAR looks incomplete
I need the MAF of a list of SNPs, I'm using the latest 1000 Genomes variant file from ANNOVAR available here: http://www.openbioinformatics.org/annovar/download/hg19_1000g2015aug.zip
But this list only has some of the RSIDs included in NCBI's dbSNP. I need the complete RSID data from 1000 genomes. For instance, the following RSIDs are not included in the ANNONVAR file, but are shown in dbSNP: rs11240777, rs12562034, rs3094315 etc
Where can I get the complete SNP list with MAF from 1000 genomes?
1 answer
You can download the 1000genome data with precalculated frequencies from ensembl https://ftp.ensembl.org/pub/grch37/current/variation/vcf/homo_sapiens/
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is this really about worldwide population frequencies or 1kg internal allele frequencies?