使用plink软件利用Fisher精确检验关联基因型和表型（GWAS）

最近看论文 Genetic subdivision and candidate genes under selection in North American grey wolves，论文里用33个狼的皮毛颜色作为表型去和基因型进行关联分析

方法部分写到

individuals. To test for associations between SNPs near coat colour genes and phenotypic variation within our samples, we performed a case/control association test using both the Fisher’s exact test for allelic association (–fisher) and the full model testing for differences in any genotypes, with permutations for assigning significance (–model –cell 0 –perm) within PLINK

最近发表的甘蓝的泛基因组论文中的关联分析也是用这种方法做的，论文

Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in _Brassica oleracea_

方法部分写到

We adopted the case–control GWAS strategy, which was widely used in disease gene mapping for humans30,31, to identify SVs that were substantially associated with different morphotypes of B. oleracea. Briefly, a GWAS analysis was performed between the case group (individuals belonging to a specific morphotype) and the control group (individuals belonging to all the other morphotypes). Significance was tested by a two-tailed Fisher’s exact test and adjusted by Bonferroni correction.

还有一篇水稻的泛基因组论文也是用的这个方法，论文

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes

方法部分写到

Fisher’s exact test was used to detect gene PAV-discrete phenotype associations, and theWilcoxon rank-sum test was used to detect gene PAV-continuous phenotype associations in R v4.0.2. P-values were adjusted using the FDR method, and a threshold of FDR < 0.05 was used to claim a significant gene PAV-phenotype association.

这个是用基因的pav矩阵来做的关联

在网上找了找plink做这个分析的教程

https://www.staff.ncl.ac.uk/heather.cordell/mres2020casecon.html

以下这个链接也可以参考

https://cloufield.github.io/GWASTutorial/06_Association_tests/#significant-loci

输入数据是一个ped文件

ped文件每列的介绍

第7列开始时基因型数据，每两列是一个位点，这个示例数据里是4个位点，所以是8列

还需要一个map文件

map格式介绍

plink做fisher精确检验的命令

plink --ped caseconped.txt --map caseconmap.txt --fisher

输出文件

把vcf文件转换成 ped和map

表型数据是3列 family id 个体id 表型，表型数据的前两列直接用vcf文件里的样本id就可以了，分隔符是Tab或者空格

plink --vcf ../rMVP/smoove_filtered.vcf --pheno pheno.txt --recode12 --allow-extra-chr --allow-no-sex --out smoove

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