Up: Component summary

VariantAnnotator

This component is not being actively maintained currently, since Annovar is updated to frequently. A simpler, more maintainable interface is available at in the component VCF2AnnotatedCSV. Another alternative is the AnnTools component, which is even easier to maintain, but so far largely unused.

This variant annotation function uses ANNOVAR which isn't allowed to be redistributed but must be downloaded directly from the author for each user ( http://www.openbioinformatics.org/annovar/ ). Installation however is as easy as uncompressing. You do need to have the appropriate database files in the reference directory, otherwise nothing will work.

The quick start guide of ANNOVAR may prove helpful.

ANNOVAR uses three main methods:

• gene-based annotation: Produces two files:
  • Location with respect to genes (exonic, intronic, intergenic, splicing site, 5'/3'-UTR, upstream/downstream of genes, invalid input
  • Amino acid changes caused by the mutation
• region-based annotation: Annotates by regions in an annotation database or in GFF3 files. Produces region annotations for each variant.
• filter-based annotation: Filter out those found in another database to find new variants

This component offers four different ways to call ANNOVAR, the first of which just calls it directly. The others use a configurable, automated sequence of filtering steps. You can select the method by specifying the annotator parameter. The scripts used by each of the extra methods are explained in ANNOVAR Accessory Programs

• The default ("annovar"): annotate_variation.pl
• Variant reduction ("variant_reduction"): variants_reduction.pl.
• Summarize ("summarize"): summarize_annovar.pl
• Table ("table"): table_annovar.pl

ANNOVAR only outputs a CSV file when using the summarize or table method. For other methods it produces non-standard VCF files that have extra columns before the standard VCF columns. It doesn't output a header. This component adds a CSV header with anonymous field names.

The first fields are called "Annotation1", "Annotation2" etc. and the rest are taken from the VCF specification, i.e. they are called CHROM, POS, ID, REF, ALT, QUAL, FILTER and INFO.

You should check ANNOVAR website to find out what the column headers mean in each case. The meaning of the extra fields might also depend on the database that is used so result interpretation must be done carefully.

Documentation for ANNOVAR itself can be mainly found on its website. Each ANNOVAR command's help file itself can be viewed with "perldoc annotate_variation.pl" (substitute the script name), for those who don't want to read the perl files directly.

ANNOVAR provides a script called "variant_reduction.pl" which can be perform multiple variant reduction steps (as does the table_annovar.pl script). It needs a two special options: the protocols to apply, and how they are applied. The exact format of these is documented in the script's own help or explained more verbosely in Variant reduction

Explanations from the ANNOVAR documentation for some gene-based annotations:

Type parameters (generics)

• T

Inputs

Outputs

Parameters

Test cases