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This article is to share with you about how to use plink to select tagSNPs, the editor thinks it is very practical, so I share it with you to learn. I hope you can get something after reading this article.

TagSNPs, called tag SNP, is used to represent a group of highly linked disequilibrium SNP loci. For a group of highly linked disequilibrium SNP loci, these loci are often inherited at the same time, and the information they contain is redundant. Only a few of these SNP loci need to be selected as representatives. This selected representative locus is called tagSNPs, and these highly linked disequilibrium SNP loci inherited together constitute haplotype. In short, tagSNP can represent all SNP sites in haplotypes.

TagSNPs plays an important role in association analysis, which greatly reduces the workload of analysis. Because tagSNP can represent a group of SNP loci, it is only necessary to analyze tagSNP, not all SNP loci.

Plink software can be used to identify tagSNPs. Since tagSNPs is based on haplotype, you need to identify haplotype block first. The command is as follows

Plink-bfile mydata-blocks

This command produces two files, plink.blocks and plink.blocks.det.

The plink.blocks content is as follows

* rs7527871 rs2840528 rs7545940* rs2296442 rs2246732* rs10752728 rs897635* rs10489588 rs9661525 rs2993510

Each line begins with a * and represents a haplotype block, followed by all SNP sites belonging to that haplotype.

The plink.blocks.det content is as follows

CHR BP1 BP2 KB NSNPS SNPS1 2313888 2331789 17.902 3 rs7527871 | rs2840528 | rs75459401 2462779 2482556 19.778 2 rs2296442 | rs22467321 2867411 2869431 2.021 2 rs10752728 | rs8976351 2974991 2979823 4.833 3 rs10489588 | rs9661525 | rs2993510

CHR denotes chromosomes, BP1 and BP2 denote the starting and ending positions of haplotype block, KB denotes the length of haplotype block, NSNPS denotes the number of SNP loci in haplotype block, and SNPS represents all SNP sites belonging to this haplotype.

Based on the results of haplotype, we can analyze the tagSNPs locus in a haplotype block, using the following method

Plink-bfile mydata-show-tags mysnps.txt

Each line in the mysnps.txt file is a SNP site, as shown in the following example

Rs7527871rs2840528rs7545940

Plink selects tagSNPs only for a set of SNP sites specified in the mysnps.txt file. This step generates two files, plink.list and plink.tags.list.

The contents of plinks.list and mysnps.txt files are similar, except that the ID of tagSNP site is added on the basis of it. The content of plink.tags.list file is as follows

SNP CHR BP NTAG LEFT RIGHT KBSPAN TAGSrs2542334 22 16694612 2 16693517 16695440 1.923 rs415170 | rs2587108

The first column of SNP sites is tagSNP, and the last column is the collection of snp sites represented by the tagSNP.

The above is how to use plink to select tagSNPs, the editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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