The massive use of Next Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes; and disease-related variants from the GWAS catalog, OMIM, COSMIC mutations, etc.)

VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied.

Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at:

User documentation

Supported input formats

Currently, the supported input formats in VARIANT are:

Look here for further information regarding the supported input formats.

Variant consequence types

VARIANT uses three different standards to code the consequence type: Sequence Ontology from OBO, Ensembl consequence type and NCBI. Learn more about the consequence types reported by VARIANT.
Here you will find information about the report generated.


VARIANT can be used in three different ways:


For downloading the latest versions of Variant, now contained inside the HPG Variant suite and known as the effect tool, please visit its page in the Open Computational Biology initiative wiki.

The following versions of the command line interface are no longer supported:

  • v1 written in Java, it can produce huge impact in memory
  • v2 new client version written C with a low memory footprint variant-2.0.tar.gz

Technical information


VARIANT uses information from different sources, here you can find a detailed list and versions used:



Global schema of the application:

Variant_fig1_480px.png (125.2 kB) Ignacio Medina, 03/14/2012 02:46 pm (28.8 MB) Ignacio Medina, 03/15/2012 08:19 pm

hpg-variant-v0.1.tar.gz (323.5 kB) Cristina Gonzalez, 06/15/2012 03:46 pm

variant-2.0.tar.gz (9.6 MB) Ignacio Medina, 07/11/2012 08:09 pm