PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data
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
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