03Genotype

Post author: zpliu
Post link: <a href="https://biocottonhub.github.io/codeHub/2021/10/28/2021-10/03Genotype/" title="03Genotype">https://biocottonhub.github.io/codeHub/2021/10/28/2021-10/03Genotype/
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发布于 Posted on 2021-10-28 修改于 Edited on 2022-11-09 In 分类于实用工具阅读量: Views: Valine:

基因型文件处理合集

1.计算两个SNP位点间的连锁度

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#* plink 文件前称
bmapFile=/data/cotton/zhenpingliu/LZP_fiberFullPopulationRNAseq/03express_gene/eQTLgenes_Allstages_340samples/indepent_eQTL/Samples_Q1000_SNPs_joint_376.filter2.Chrs.short
plink --bfile $bmapFile --ld SNP303009 SNP304796

2.提取SNP对应的坐标信息

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#* 提取任意SNP对应的坐标信息
plink --bfile $bmapFile --snp SNP303009 --make-bed
plink --bfile $bmapFile --extract SNPlist.txt --make-bed