Segmented HAPlotype Estimation and Imputation Tool

ShapeIT is a fast and accurate haplotype inference software with several notable features:

• Linear complexity with the number of SNPs/individuals in the sample.
• Phasing whole chromosome at once is possible.
• Mixed samples of Trios, Duos and Unrelated are supported.
• Phasing uncertainty is captured by the graphical model and easy to propagate in downstream analysis.
• Phasing is multi-threaded to decrease computational times.

ShapeIT was developed in C++ by Olivier DELANEAU (olivier.delaneau at gmail.com) under the supervision of Jean-Francois ZAGURY (zagury at cnam.fr). It uses the Standard Template Library (STL) and the POSIX thread library (pthread). For any technical issues with the software please feel free to contact Olivier DELANEAU.

A short description of how ShapeIT works:

The paper to cite if ShapeIT is used.