How I could get the MAF from a SNPs list?

Question

[vgenepi]

Hi everyone! I would like to get the MAF of a list of SNPs. Human. Europeans. I have already followed the instructions fouded in similar post here using ensembl and ucsc database without succeeding. My SNPs are in Build 37 and the position is already known.

Thanks in advance

[Kevin Blighe]

You will have to provide more information, such as the format in which your data is currently? - Plink?; VCF; FASTA?

The MAF calculation is obviously just counting the called alleles at each position and obtaining the percentage (i.e. frequency) of the less common allele.

A A A A A G A A A A

A= 90%

G=10%

G is the minor allele, with MAF 0.1

[cpad0112]

For matching variants, CEU data from Hapmap3 will be helpful for European population MAF. Try working with vcf from hapmap3 ceu population and dbSNP currently stores allele frequency by population.

[vgenepi]

Thanks a lot for the reply! I have an Excel file from an array with those variables: IlmnID,Name,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq, GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand, SourceSeq,TopGenomicSeq,BeadSetID.

I used PLINK once to estimate the MAF, but in that case I had all the files that it needs.

Thanks in advance

[Kevin Blighe]

You just want that MAF from the 1000 Genomes Phase III NFE (Non-Finnish European) or the HapMap CEU?

As you appear to have chromosome and position, use ANNOVAR. I can help you with the coding and set-up, if you wish.

Also take a look at SNP nexus

[vgenepi]

Thanks, I tried with SNP nexus but I loose too many information, as it has not all the SNP information that are in my list.

And actually, I need MAF from 1000 GP and not from HapMap. Is there another data bank as SNP Nexus that use the 1000 GP data base? Thanks

[Kevin Blighe]

Okay, in that case, use Annovar. It annotates allele frequencies from:

• 1000 Genomes Phase III (all main populations)
• Greater Middle East project
• Exome Variant Server