经过WGS上游分析之后，会产生类似于样本对应的*_hg38_multianno.txt文件：

然后通过合并txt文件，调整数据，生成一个多样本融合txt文件：

一、通过脚本合并txt文件

                for id in *hg38_multianno.txt

        do

 add=${id##*/};add=${add%%.*};awk '{if (NR==1) {print $0, "Tumor_Sample_Barcode"}; if (NR>1) {print $0,"'"$add"'"}}'  $id >> merged.hg38_multianno.txt

        done

二、调整数据

            1、取出行名： 

 cat merged.hg38_multianno.txt |head -1 > merg.head.txt

                2、调整merge文件

cat merged.hg38_multianno.txt|head-1>merg.head.txt

cat merged.hg38_multianno.txt|grep-v"Tumor_Sample_Barcode">merged.hg38_multianno.txt2

cat merg.head.txt merged.hg38_multianno.txt2>merged.hg38_multianno.txt3

awk '{print$1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$NF}' merged.hg38_multianno.txt3>merged.hg38_multianno.txt.final

三、在R中进行下游分析    

    1、生成maf文件

annovarToMaf(annovar = "Annovar/merged.hg38_multianno.txt.final",Center = NULL,refBuild = "hg38",tsbCol = 'Tumor_Sample_Barcode',sep = " ",MAFobj = T,basename = "merged.hg38_multianno.fianl")

    2、读入maf文件

merged.hg38_multianno_maf <- read.maf(maf = "merged.hg38_multianno.fianl.maf")

    3、作maf文件统计概要图

plotmafSummary(maf = merged.hg38_multianno_maf , rmOutlier = T , addStat = "median" , dashboard = T , titvRaw = F)

    4、绘制初版瀑布图

                        oncoplot(maf = merged.hg38_multianno_maf,draw_titv = T)

5、参考文章

    https://www.haomeiwen.com/subject/kjqtmhtx.html

    https://blog.csdn.net/qq_27390023/article/details/122307143

    https://www.jianshu.com/p/90ddc0da1954