stay In the first two sections , We compared the differences vcf Use of annotation software , And convert the demerit recorded after the annotation into maf File format , because snpeff The comment result cannot be converted to maf, So we will compare later ANNOVAR、VEP、GATK Funcatator The results of the annotation are merged maf file . First, load the obtained results into R In language , And then use maftool visualization , The code is as follows ：
Read in the data
rm(list = ls())
require(maftools)
options(stringsAsFactors = F)
## annovar
annovar.laml <- annovarToMaf(annovar = "./7.annotation/annovar/annovar_merge.vcf",
refBuild = 'hg38',
tsbCol="Tumor_Sample_Barcode",
table="refGene",
MAFobj = T)
## gatk
# gatk.laml = read.maf(maf="gatk/gatk4.1.4.0_merge.maf")
library(data.table)
tmp=fread('./7.annotation/funcatator/funcatator_merge.maf')
gatk.laml = read.maf(maf = tmp)
## vep
vep.laml = read.maf(maf="./7.anRead more here: Source link
