A library and toolset for working with human genetic variation data

PLINK/SEQ is an open-source C/C++ library (input VCF file) for working with human genetic variation data. The specific focus is to provide a platform for analytic tooldevelopment for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library couldin principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs.

A number of interfaces to the core library are available, providing different ways to access a PLINK/SEQ project:

• Command line tool: pseq provides easy access to some of the most common functions of the library (e.g. loading and querying data) and also implements a number of useful statistical procedures (e.g. to summarise datasets, perform phenotype-genotype association tests).
• R package for statistical computing: Use R as an interface to the dynamically-linked C/C++ extension library. This provides convenient access to the powerful statistical and visualisation tools available in R.
• Web-browser: an exome-centric table-browser provides a simple, interactive tool for searching and reporting on a project's variant, genotypic and phenotypic data and meta-data.
• C/C++ API: alternatively, one can use the C/C++ library API directly, to build analysis packages or other tools.