Question: GWAS dataset calculating MAF for European dataset
0
gravatar for victoria_mulcahy
8 months ago by
victoria_mulcahy10 wrote:

How does frequency of existing variant in the combined 1000 genome European data from Variant effector predicator website equate to MAF. I have a SNP data from GWAS data and need to find the MAF for each of the SNPs. Thank you

gwas maf • 175 views
ADD COMMENTlink written 8 months ago by victoria_mulcahy10
0
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Hi Victoria, can you please clarify the format of your data, currently? Per any given variant, MAF can be applied specifically to any population, i.e., MAF in the global population, MAF in the Irish population, MAF among sub-Saharan Arficans, et cetera.

ADD COMMENTlink written 8 months ago by Kevin Blighe67k

Dear Kevin, I have a European dataset with SNP data and need to get the MAF for each SNP. I have a lot of data from a GWAM study. Headings are; CHR SNP BP ref_allele alt_allele sample_size case_proportion Thank you

ADD REPLYlink written 8 months ago by victoria_mulcahy10

Hi, in that case, you already have enough information to calculate the MAF in your own cohort of patients / samples. However, if you want the MAF for your variants from the large public databases, then you could use Ensembl VEP or ANNOVAR. Both of these will take some time to set up, though. There are other solutions, too.

ADD REPLYlink written 8 months ago by Kevin Blighe67k

As in;

If (AF < 0.5) then MAF = AF

if (AF > 0.5) then MAF = 1.0 - AF

ADD REPLYlink written 8 months ago by victoria_mulcahy10

More or less, yes! That is, this is your study-specific MAF.

ADD REPLYlink written 8 months ago by Kevin Blighe67k
1

Thank you for your help!

ADD REPLYlink written 8 months ago by victoria_mulcahy10

If you find that the AF is > 0.5, though, then you also have to remember to flip the order of the REF and ALT alleles. These situations are quite common and may arise due to this problem: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.

I would also verify that some of the AFs in your VCF are actually valid by literally counting across all samples... got to be sure in bioinformatics!

ADD REPLYlink written 8 months ago by Kevin Blighe67k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1273 users visited in the last hour