Question: MAF in QC of genetic association study
1
gravatar for GenMD
3.3 years ago by
GenMD10
GenMD10 wrote:

Hello,

I'm using plink for QC. I have two questions re MAF:

1. My understanding is that plink (plink --file data --freq) will estimate the MAF based on the data and accordingly in the QC it will remove SNPs based on its own MAF estimates. Is this correct?

2. What is the standard for removing SNPs based on MAF threshold? Is it MAF estimates based on the data (as above)? or is it based on a general population e.g using 1000Genome data or similar?

 

myposts • 1.2k views
ADD COMMENTlink modified 3.3 years ago by Maxime Lamontagne2.1k • written 3.3 years ago by GenMD10
2
gravatar for Maxime Lamontagne
3.3 years ago by
Québec
Maxime Lamontagne2.1k wrote:

1. Plink will produce a file with the MAF for each SNP (plink.frq). You need to select which SNPs you want to remove.

2. In GWAS study: MAF < 1 or 5%.

ADD COMMENTlink written 3.3 years ago by Maxime Lamontagne2.1k

Thank you. Yes, I understand that. My question though how does plink calculate the MAF? is it based on my data or is it an estimate from the general population?

ADD REPLYlink written 3.3 years ago by GenMD10
1

Your data                  

ADD REPLYlink written 3.3 years ago by Maxime Lamontagne2.1k
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