Entering edit mode
10.1 years ago
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
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.