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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 aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
You can try it online or clone it from the GitHub repository.
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]
More info about Variant Effect is available through its tutorial.
Genome-wide association study (GWAS) analysis have been used for many years in Genotype Arrays with Plink, here we continue the goal of PLink but using genotypes from 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} ...
More info about Variant GWAS is available through its tutorial.
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 } ...
More info about Variant VCF Tools is available through its tutorial.
The user's guide 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.
- OpenMP
- MPI
- REST Web Services
Published at Nucleid Acids Research.