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#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
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