PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be familiar to PLINK users.
PLINK/SEQ boasts an impressive feature set for a project still in the beta testing phase. It supports several data types (multiallelic, phased, imputation probabilities, indels, and structural variants), and can handle datasets much larger than what can fit into memory. PLINK/SEQ also comes bundled with several reference databases of gene transcripts and sequence & variation projects, including dbSNP and 1000 Genomes Project data.
As with PLINK, the documentation is good, and there's a tutorial using 1000 Genomes Project data.
PLINK/SEQ - A library for the analysis of genetic variation data