Is it possible to add all possible VCF annotations in one command using ANNOVAR ?

Question

[kay]

Hello

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)
annotate_variation.pl -buildver hg19 ex1.avinput humandb/

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

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

table_annovar.pl 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

[igor]

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

[kay]

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 
annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand ex1.avinput humandb/ 

#filter based anno 
annotate_variation.pl -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 ?

annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand -filter -dbtype 1000g2015aug_all -maf 0.01 ex1.avinput humandb/

[igor]

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

[harold.smith.tarheel]

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 'table_annovar.pl'.