论文
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
西红柿NG_superPan正文.pdf
数据分析的代码
论文里提供了绝大部分的数据处理代码,很好的学习材料,今天的推文我们学习一下论文中确定GWAS分析阈值的方法,论文里写到
The genome-wide significance thresholds (7.58 × 10−7) were determined using a uniform threshold of 1/n, where n is the effective number of independent SNPs and SVs calculated using the Genetic type 1 Error Calculator (v.0.2)
但是没有在论文里找到对应的这部分代码
在另外一篇黄瓜的Nature Communications的论文里也提到了这个方法,论文是
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
方法部分写到
The genome-wide significance threshold (3.46 × 10−5) was determined by a uniform threshold of 1/n, where n was the effective number of independent SVs calculated using Genetic type 1 Error Calculator (v0.2)
GEC软件的主页
http://pmglab.top/gec/#/download
帮助手册
http://pmglab.top/gec/data/archive/v0.2/UserManualV0.2.pdf
软件对应的论文
Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets
下载下来直接解压就能用
这个软件的全称是 GEC: The Genetic Type I error calculator
首先使用plink把vcf文件转换成bed文件
/biotools/plink19/plink --vcf input.vcf --make-bed --out abc
abc是输出文件的前缀,我把这些文件输出到了outputfolder这个文件夹下
计算有效位点数
java -jar -Xmx8g ~/biotools/GEC/gec/gec.jar --effect-number --plink-binary outputfolder/abc --genome --out test1
生成了一个文件 test1.sum,里面的信息有
能得到结果,不太确定整个过程有没有错误,如果有懂行的大佬欢迎留言指教!
这个应该是专门为人类数据分析准备的,计算过程会输出,不知道换成其他物种是否有参数需要更改
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