#purpose: re-annotate VCF with table_annovar.pl 
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03 humandb/ 
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 humandb/ 
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp30a humandb/


#set env
annovar_adr="/home/zhanghl/supporting_softwares/annovar/annovar"
infolder="/path/mutect2_result"
outfolder="/path/annovar_result"
annovardb=$annovar_adr/humandb

for sample in `cat /path/sample_list`;do 
/home/zhanghl/local/perl_install/bin/perl $annovar_adr/table_annovar.pl  $infolder/${sample}.mutect2.filter.vcf \
$annovardb/ \
-buildver hg19 \
-out $outfolder/$sample \
-remove \
-protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a \
-operation gx,r,f,f,f \
-nastring . \
-csvout \
-polish \
-xref /home/zhanghl/supporting_softwares/annovar/annovar/example/gene_fullxref.txt
done