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Maf Parameters In Quality Control

I am conducting a GWAS study using PLINK and the dataset I have been given has almost 130 000 SNP's. I have been asked to perform QC of the data, with parameters on MAF, Call rate and HWE.

The stated MAF is >=0.5. However, when this test is performed, I am only left with 13 SNP's.

Is this an expected occurrence or not? Thanks

maf qc plink gwas
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written by tom.d.brocklehurst • tom.d.brocklehurst

Use 0.05. MAF >= 0.05

You can't remove SNPs with a MAF greater than 0.5, because it do not exist. The MAF is <= 0.5. Your 13 SNPs probably have a MAF of 0.5.

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written by Maxime Lamontagne Maxime Lamontagne

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