Question: How Plink LD-pruning selects which one of the pair SNPs in LD.
0
gravatar for dadoudou
2.8 years ago by
dadoudou0
Hong Kong
dadoudou0 wrote:

I am using plink to ld-pruning SNPs. But I wonder why plink always produce the same pruning results, even when I add a random seed.

Let's suppose, SNPs A and B are in LD.  They can be also in LD with other SNPs. The SNPs in LD with A and the SNPs with B might be different. Thus, the first choice of A or B might produce different pruning SNP set. So, LD-pruning should produce a random result, really?

Here, I worry that Plink always produces a same result, it will produce a bias? Thank you for comments.

snp plink ld-pruning • 3.2k views
ADD COMMENTlink modified 2.8 years ago by chrchang5232.8k • written 2.8 years ago by dadoudou0
1
gravatar for chrchang523
2.8 years ago by
chrchang5232.8k
United States
chrchang5232.8k wrote:

PLINK keeps the SNP with higher minor allele frequency, if the two MAFs are not identical.  When there is a tie, the first SNP is kept.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by chrchang5232.8k
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