gwas snp 和_GWAS学习笔记4－－－SNP过滤

1:缺失比例(Missing

rates)：(

GENO > 0.05 )

Shortly we will

apply more stringent criteria, such that GENO > 0.05. In this

case, 0.05*89 = 4.45 samples, meaning that if a SNP is missing in

4.45 more more samples, that SNP will be removed from the

dataset.

2:最小等位基因频率(Minor

Allele frequencies)(

MAF< 0.03 如果SNP较多可以设置为MAF<0.05)

MAF

is the Minor Allele Frequency. It can be used to exclude SNPs which

are not informative because they show little variation in the

sample set being analyzed. For instance, if a SNP shows variation

in only 1 of the 89 individuals, it is not useful statistically and

should be removed.

3:Removing SNPs

out of Hardy-Weinberg equilibrium(p-value > 10−6 -

10−4

)

Population

genetic theory suggests that under ‘normal’ condit