[Software] variation annotation tools: annovar

annovar provides three ways Comment

First, based on comments given gene mutation, variation to see whether the impact of changes in protein-coding genes defined support system: RefSeq genes, UCSC genes, ENSEMBL genes, GENCODE genes, AceView genes, or many other gene definition systems.

Second, based on the comment area to see if a particular mutation in the region of the genome

Third, to see whether a mutation in a particular database, such as a filter-based annotation dbSNP

annotate_variation.pl main
table_annovar.pl common program notes

key parameter

—-buildver    数据库版本, 如hg19
—-protocol    refGene, exac03

anno_refgene.sh

#!/bin/bash

name=$1
/rawdata/Zhangyu/software/ANNOVAR_latest/annovar/table_annovar.pl $name 
/rawdata/Zhangyu/software/ANNOVAR_latest/annovar/humandb 
-buildver hg19 
-otherinfo 
-remove 
-nastring . 
-protocol refGene 
-operation g 
--outfile ${name}.annovar

13 20797176 21105944 0 - comments: a 342kb deletion encompassing GJB6, associated with hearing loss

annovar_latest.sh

#!/bin/bash

name=huaxi-7.varscan.vcf
/rawdata/Zhangyu/software/ANNOVAR_latest/annovar/table_annovar.pl $name 
/rawdata/Zhangyu/software/ANNOVAR_latest/annovar/humandb 
-buildver hg19 
-otherinfo 
-remove 
-nastring . 
-protocol refGene,SAOdbSNP150,cosmic83,gnomad_exome,NovoDb_WES_2573,NovoDb_WGS_568,clinvar_20170905,HGMD,genomicSuperDups,gff3 
-operation g,f,f,f,f,f,f,f,r,r 
    
    
     
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     【software】变异注释工具：annovaran class="se">

     
     --gff3dbfile hg19_rmsk.gff 
     
     

     
     --vcfinput 
     
     

     
     --outfile 
     
     ${
     
     name
     
     }.annovar

    
    

TJ cluster annovar comments

name=$1
/PUBLIC/software/HUMAN/ANNOVAR_2017Jun08/table_annovar.pl ./${name} 
/TJNAS01/OBD/Zhangyu/software/annovar_new_db_all_2019.1.8 
-buildver hg19 
-otherinfo 
-remove 
-nastring . 
-protocol refGene,avsnp150,SAOdbSNP150,1000g2015aug_all,exac03,esp6500siv2_all,gnomad_exome,NovoDb_WES_2573,NovoDb_WGS_568,cosmic83,clinvar_20170905,HGMD,ljb26_pp2hvar,ljb26_pp2hdiv,ljb26_sift,gerp++gt2,caddgt10,genomicSuperDups,gff3 
-operation g,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,r,r 
--gff3dbfile hg19_rmsk.gff 
--outfile ${name}.annovar

TJ cluster annovar comment, input for the VCF

name=$1
/PUBLIC/software/HUMAN/ANNOVAR_2017Jun08/table_annovar.pl ./${name}.vcf 
/TJNAS01/OBD/Zhangyu/software/annovar_new_db_all_2019.1.8 
-buildver hg19 
-otherinfo 
-remove 
-nastring . 
-protocol refGene,avsnp150,SAOdbSNP150,1000g2015aug_all,exac03,esp6500siv2_all,gnomad_exome,NovoDb_WES_2573,NovoDb_WGS_568,cosmic83,clinvar_20170905,HGMD,ljb26_pp2hvar,ljb26_pp2hdiv,ljb26_sift,gerp++gt2,caddgt10,genomicSuperDups,gff3 
-operation g,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,r,r 
--gff3dbfile hg19_rmsk.gff 
--vcfinput 
--outfile ${name}.annovar

About handling of indel

There is no generally accepted way to describe the indel.

As users, we should do the following: (1) split VCF files to ensure that each line contains only one variation; (2) left-normalize all VCF files; (3) the use of ANNOVAR comments

Therefore, use the command:

bcftools norm -m-both -o ex1.step1.vcf ex1.vcf.gz

bcftools norm -f human_g1k_v37.fasta -o ex1.step2.vcf ex1.step1.vcf

The first command is detected variation allels division multiple separate lines, the second command to run real left-normalization. (Sometimes the first command may not appear variation can be broken down, despite the presence of these mutations in the file, in which case, you can use vt program in place)

reference:

ANNOVAR mutation comments

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