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ZhihaoXie / ctDNA_mutation Public

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ctDNA_mutation

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run7_annovar.sh

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10 lines (6 loc) · 371 Bytes

Breadcrumbs

ctDNA_mutation

/

run7_annovar.sh

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10 lines (6 loc) · 371 Bytes

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#!/bin/bash

vcf=`readlink -f $1`

outprefix=$2

# annovar

annovar_dir="/home/xiezhihao/biosoft/annovar"

perl $annovar_dir/table_annovar.pl $vcf $annovar_dir/humandb/ -buildver hg19 -out $outprefix -remove -protocol refGene,cytoBand,cosmic70,snp138,clinvar_20180603,1000g2015aug_all,esp6500siv2_all,dbscsnv11,dbnsfp35c -operation g,r,f,f,f,f,f,f,f -nastring . -vcfinput

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