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Extracting LD SNPs using PLINK2

I've been using plink1.9 to extract LD SNPs for a list of SNPs stored in file as follows:

plink1.9 --bfile 1kg_phase1_all --ld-window-r2 0.8 --ld-window-kb 100 --ld-window 1000000 --ld-snp-list snps.txt --r2 yes-really --out gwas --exclude plink_output/gwas.dupvar2

How to convert this command to plink2?

Tried to move this to plink2 and it seems like the semantics has changed dramatically, and I couldn't figure it out. Would appreciate it if someone versed on plink2 could help me out with this.

snps ld plink1.9 plink2
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written by Sanjar Sanjar

2 answers

It turns out that the command for extracting LD SNPs has not been implemented in PLINK2 yet.

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written by Sanjar Sanjar

Instead of plink, would you prefer to use other alternatives like Ensembl's LD Calculator?

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written by austin7923 • austin7923

I haven't used it before. I thought that plink is the "gold standard". Do you recommend it?

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written by Sanjar Sanjar

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