vtools supports the generation of an ANNOVAR input file through the ANNOVAR.fmt format. In addition, there are two ANNOVAR format files (ANNOVAR_variant_function.fmt and ANNOVAR_exonic_variant_function.fmt) that support the import of ANNOVAR generated annotations.

Example of running annovar on variants in vtools and importing the resulting annotations

# export all variants in the variant table to an annovar file (an input file for annovar)
vtools export variant ANNOVAR.input --format ANNOVAR

# run annovar to generate annotation files
# see http://www.openbioinformatics.org/annovar/ for help
perl annotate_variation.pl -geneanno ANNOVAR.input -buildver hg19 humandb/

# import annovar annotations using a separate format for each of the two annovar annotation files
vtools update variant --format ANNOVAR_exonic_variant_function --from_file ANNOVAR.input.exonic_variant_function --var_info mut_type function genename
vtools update variant --format ANNOVAR_variant_function --from_file ANNOVAR.input.variant_function --var_info region_type region_name

You now have the following fields: region_type, region_name, genename, mut_type, and function added as annotations to your variants in vtools.

A description of the used annotation files are below.

ANNOVAR.fmt

vtools show format ANNOVAR
Format:      ANNOVAR
Description: Input format of ANNOVAR. No genotype is defined.

Columns:
  1            chromosome
  2            position (1-based)
  3            end position
  4            reference allele
  5            alternative allele
  6            optional column

variant:
  chr          Chromosome
  pos          1-based position
  ref          Reference allele, '-' for insertion.
  alt          Alternative allele, '-' for deletion.

Format parameters:
  comment_string Output one or more fields to the optional comment column of this
               format. (default: )

ANNOVAR_variant_function.fmt

vtools show format ANNOVAR_variant_function
Format:      ANNOVAR_variant_function
Description: Output from ANNOVAR for files of type "*.variant_function", generated
  from command "path/to/annovar/annotate_variation.pl annovar.txt
  path/to/annovar/humandb/". This format imports chr, pos, ref, alt
  and ANNOVAR annotations. For details please refer to
  http://www.openbioinformatics.org/annovar/annovar_gene.html

Columns:
  None defined, cannot export to this format

variant:
  chr          Chromosome
  pos          1-based position
  ref          Reference allele, '-' for insertion.
  alt          Alternative allele, '-' for deletion.

Variant info:
  region_type  The genomic region type (i.e., intergenic, ncRNA_intronic, etc) where
               this variant lies.

Other fields (usable through parameters):
  region_name  Genomic region name that corresponds to the region_type.  If the
               variant lies in an intergenic region, this field will
               specify the closest known regions upstream and
               downstream of this variant.

Format parameters:
  var_info     Fields to be outputted, can be one or both of region_type and
               region_name. (default: region_type)

ANNOVAR_exonic_variant_function.fmt

vtools show format ANNOVAR_exonic_variant_function
Format:      ANNOVAR_exonic_variant_function
Description: Output from ANNOVAR, generated from command
  "path/to/annovar/annotate_variation.pl annovar.txt
  path/to/annovar/humandb/". This format imports chr, pos, ref, alt
  and ANNOVAR annotations. For details please refer to
  http://www.openbioinformatics.org/annovar/annovar_gene.html

Columns:
  None defined, cannot export to this format

variant:
  chr          Chromosome
  pos          1-based position
  ref          Reference allele, '-' for insertion.
  alt          Alternative allele, '-' for deletion.

Variant info:
  mut_type     the functional consequences of the variant.

Other fields (usable through parameters):
  genename     Gene name (for the first exon if the variant is in more than one
               exons, but usually the names for all exons are the
               same).
  function     the gene name, the transcript identifier and the sequence change in
               the corresponding transcript

Format parameters:
  var_info     Fields to be outputted, can be one or both of mut_type and function.
               (default: mut_type)