經(jīng)過WGS上游分析之后，會產(chǎn)生類似于樣本對應(yīng)的*_hg38_multianno.txt文件：

然后通過合并txt文件，調(diào)整數(shù)據(jù)，生成一個(gè)多樣本融合txt文件：

一、通過腳本合并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、調(diào)整數(shù)據(jù)

? ? ? ? ? ? 1、取出行名：?

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

? ? ? ? ? ? ? ? 2、調(diào)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中進(jìn)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、讀入maf文件

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

? ? 3、作maf文件統(tǒng)計(jì)概要圖

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

????4、繪制初版瀑布圖

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

5、參考文章

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

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

? ??http://www.itdecent.cn/p/90ddc0da1954