Annovar注释的突变文件转MAF对象

maftools可以读入Annovar注释的突变文件，生成成MAF对象，方便下游的突变分析。

1. 合并不同样本的突变文件，加上样本编号

原始的vcf文件经过Annovar软件注释后会生成注释好的.vcf以及.txt文件。

#每个样品一个文件夹，下面有annovar注释的文件

for id in `find ./ -name *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

# 根据文件名解析出样本编号，较为复杂。

## 去掉多余的行和列
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

2. 读入合并后的数据，生成MAF对象

# if (!requireNamespace("BiocManager", quietly = TRUE))
#   install.packages("BiocManager")
# 
# BiocManager::install("maftools")

library(maftools)
# ls("package:maftools")

var.annovar <-"path/to/your/file"

# 生成MAF对象。注意分隔类型             
var.annovar.maf = annovarToMaf(annovar = var.annovar, 
                               refBuild = 'hg38',
                               sep = " ",
                               tsbCol = 'Tumor_Sample_Barcode',
                               MAFobj = TRUE)

oncoplot(maf = var.annovar.maf, draw_titv = TRUE)