Question: Is it possible to add all possible VCF annotations in one command using ANNOVAR ?
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4.6 years ago by
United States
krithika.gu280 wrote:


So I know Annovar documentation talks about gene-based, region-based and filter-based annotations.

I am interested in annotating my input VCF file with ALL these possible annotations. Annovar documentation provides 3 different examples for gene-based, region-based and filter-based annotations

Examples by annovar

#gene-based annotation of variants in the varlist file (by default --geneanno is ON) -buildver hg19 ex1.avinput humandb/

#region-based annotate variants -regionanno -buildver hg19 -dbtype cytoBand ex1.avinput humandb/ -regionanno -buildver hg19 -dbtype gff3 -gff3dbfile tfbs.gff3 ex1.avinput humandb/

#filter rare or unreported variants (in 1000G/dbSNP) or predicted deleterious variants -filter -dbtype 1000g2015aug_all -maf 0.01 ex1.avinput humandb/ -filter -buildver hg19 -dbtype snp138 ex1.avinput humandb/ -filter -dbtype dbnsfp30a -otherinfo ex1.avinput humandb/

I have also tried this, another example given by Annovar, but it does not annotate with all possible annotations: example/ex2.vcf humandb/ -buildver hg19 -out myanno -remove \
    -protocol refGene,cytoBand,genomicSuperDups,esp6500siv2_all,snp138,avsnp144,\
    ljb26_all,knownGene -operation g,r,r,f,f,f,f,f -nastring . -vcfinput

Is there a way to perform gene-based, region-based and filter-based annotations (bascially ALL possible annotations) in one command ?

Any examples would help

Thanks, K

annovar • 1.9k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.6 years ago by krithika.gu280

What do you mean doesn't do all possible annotations? Isn't that exactly what it does?

ADD REPLYlink written 4.6 years ago by igor12k

Annovar groups annotations into 3 types (gene-based, region-based, filter-based) . It looks like there are 3 different commands to do various types of annotations.

#region-based anno -regionanno -buildver hg19 -dbtype cytoBand ex1.avinput humandb/ 

#filter based anno -filter -dbtype 1000g2015aug_all -maf 0.01 ex1.avinput humandb/

My question is - is it possible to do all 3 types of annotations in one single command ? Something like this ? -regionanno -buildver hg19 -dbtype cytoBand -filter -dbtype 1000g2015aug_all -maf 0.01 ex1.avinput humandb/
ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by krithika.gu280

That is what -operation parameter is for. You give it g/r/f for different annotation types.

ADD REPLYlink written 4.6 years ago by igor12k

It would be useful to paste a few lines of your output that indicate exactly which annotations are present in your table but not included when running ''.

ADD REPLYlink written 4.6 years ago by harold.smith.tarheel4.6k
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