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.
# 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.
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: )
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)
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)