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.

The HPG-VARIANT suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. The implementation will be develop using High Performance Computing technologies to provide the best performance possible.

You can try it online at http://variant.bioinfo.cipf.es or download it from http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads.

Current features

Currently supported features include:

Variant effect (formerly known as VARIANT)

Resolving the effect of variants is a crucial step in variant analysis, here we present a CLI client that use remote RESTful Web Services to get the consequence types. This CLI client is based in http://variant.bioinfo.cipf.es/ Basic command line is like this:

hpg-var-effect {--vcf-file} [--exclude | --url | --num-threads]

You can visit this page for more info More info about effect

Genomic statistical analysis have been used for many years in Genotype Arrays with Plink, here we continue the goal of PLink but using genotypes form VCF. All this methods use modern HPC technologies to speed up performance. Basic command line is like this:

hpg-var-gwas { assoc | tdt | ... } {--ped-file} ...

You can visit this page for more info More info about genomic analysis

Variant Call Format management tools

Accelerates the preprocessing of VCF files, allowing to filter their entries but several criteria, merging multiple files into one or splitting one into several files, and retrieving statistics related to variants and samples.

hpg-var-vcf { filter | merge | split | stats } ...

You cant visit this page for more info More info about VCF Tools

Feature plan

Feature supported in the future are:

Variant calling

Current implementations of variant calling takes several hours, here we have re-implemented most accepted algorithms using HPC technologies: GATK and SAMtools mPileup

hpg-var-call {--gatk | --mpileup} {--bam-file}

Functional analysis

Functional analysis can be also implemented in order to study the enrichment of mutations in different functional modules

hpg-var-functional {--go | --disease} {--vcf-file}

You can visit this page for more info More info about functional analysis

Pathway analysis

Systmes biology provide a new framework for the study and analysis the variant or set of variants in diffents paths of a pathaway

hpg-var-pathway {--reactome | --interactome} {--vcf-file}

You can visit this page for more info More info about Pathway Analysis

Manual

The user's manual describes the installation and (optional) configuration processes. It also contains information about the goal and usage of each tool of HPG Variant. It is under continuous development, at the same pace as the application.

Download

Current and previous releases are available at the following link: http://docs.bioinfo.cipf.es/projects/hpg-variant/files

Technologies used

  • OpenMP
  • RESTful web services