vcf文件annovar的注释结果绘制瀑布图maftools分析

1.vcf文件annovar注释:

table_annovar.pl  154.raw.somatic.vcf.gz   humandb/hg38/ -buildver hg38 -out  154 -remove -protocol \
 refGene,cosmic70,nci60,esp6500siv2_all,clinvar_20210501,1000g2015aug_all,1000g2015aug_eas,1000g2015aug_sas,avsnp150,gwasCatalog,ljb26_all,cytoBand,dgvMerged,phastConsElements100way,genomicSuperDups -operation g,f,f,f,f,f,f,f,f,f,f,r,r,r,r -nastring . -vcfinput

2. 提取必要的信息

 for i in *.hg38_multianno.txt
  do
      sample=`echo $i|awk -F '.' '{print $2}'`
      cut -f '1-10' $i|sed '1d'|sed "s/$/\t${sample}/">>all_sample.txt
  done
  
  sed -i '1s/^/Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tTumor_Sample_Barcode\n/' all_sample.txt

3. 读入数据，利用maftools绘图

library(maftools)
  var_maf= annovarToMaf(annovar = "all_sample.txt", 
                              Center = 'NA', 
                              refBuild = 'hg38', 
                              tsbCol = 'Tumor_Sample_Barcode', 
                              table = 'refGene',MAFobj =T,
                              sep = "\t")

  plotmafSummary(maf = var_maf, rmOutlier = TRUE, addStat = 'median')

oncoplot(maf = var_maf, top = 30, fontSize = 12 ,showTumorSampleBarcodes = F )

发表于 2022-01-04 13:04
阅读 ( 3212 )
分类：重测序

vcf文件annovar的注释结果绘制瀑布图maftools分析

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