连锁不平衡LD

step1：从conda上下载plink2

conda install bioconda::plink2

step2：从Resources中的1000 Genomes phase 3下载all_hg38.pgen.zst、all_hg38_rs.pvar.zst 、hg38_corrected.psam

plink2软件的教程: https://www.cog-genomics.org/plink/2.0/

从Resources中的1000 Genomes phase 3下载all_hg38.pgen.zst、all_hg38_rs.pvar.zst 、hg38_corrected.psam，并将all_hg38_rs.pvar.zst 改名为all_hg38.pvar.zst ，hg38_corrected.psam改名为hg38.psam

step3：解压pgen

plink2 --zst-decompress all_hg38.pgen.zst > all_hg38.pgen.zst

step4：把pgen转化成bed,bim,fam

plink2 --pfile all_hg38 vzs -- max-alleles 2 -- make-bed -- out all_hg38_test -- allow-extra-chr

step5：从hg38_corrected.psam筛选出欧洲人，将#IID保存为 eur_iid.txt

plink2 --bfile all_hg38_test --keep eur_IID.txt --make-bed --out all_hg38_test2 -- allow-extra-chr

step6：将需要的SNP保存成SNP.txt

plink2 --bfile all_hg38_test2 --extract SNP.txt --make-bed --out test -- allow-extra-chr

step7：排除重复的SNP

plink2 --bfile test --rm-dup force-first list ---make-bed --out test_nodups -- allow-extra-chr

step8：LD

plink2 --bfile test_nodups --indep-pairwise 500 10 0.1 -- allow-extra-chr

得到plink2.prune.in文件
参数含义见文档: https://www.cog-genomics.org/plink/2.0/ld