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#!/usr/bin/bash purpuse: combine annovar results and convert it to MAFtools format #combination infolder="/home/zhanghl/data_3/workshop/yelianhua/wes/annovar_result" outfolder="/home/zhanghl/data_3/workshop/yelianhua/wes/annovar_result" for sample in `cat /home/zhanghl/data_3/workshop/yelianhua/wes/sample_list`;do cut -f '1-10' $infolder/${sample}.hg19_multianno.txt | sed '1d'|sed "s/$/\t${sample}/" >> $outfolder/all_annovar done grep -P "\texonic\t" $outfolder/all_annovar > $outfolder/all_annovar2 /home/zhanghl/local/perl_install/bin/perl /home/zhanghl/supporting_softwares/to-maftools/to-maftools.pl $outfolder/all_annovar2 #将文件转换为maf格式 #convertion require(maftools) var.annovar.maf <- annovarToMaf(annovar = "all_annovar3", Center = 'CSI-NUS', refBuild = 'hg19',tsbCol = 'Tumor_Sample_Barcode', table = 'refGene') write.table(var.annovar.maf,file="var_annovar_maf",quote= F,sep="\t",row.names=F) var_maf = read.maf(maf ="var_annovar_maf")
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