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SHAPEIT (estimation of haplotypes)

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As stated on the SHAPEIT home page, it is (fast and accurate) software for "estimation of haplotypes (aka phasing) from genotype or sequencing data."  It can be used in combination with IMPUTE2.

See the SHAPEIT Software Versions page (or choose the corresponding tab above) for a list of systems on which the software has been installed.

Note that SHAPEIT can run on multple cores through the threads option, but, parallelism is restricted to a single compute node. SHAPEIT jobs should request computing resources with a directive of the form:

#PBS -l nodes=1:ppn=x

where x depends on the hardware being used and the batch policies in place. You can discuss the issues involved with WestGrid technical support by sending email to

To ensure that the number of cores requested through the ppn parameter matches the number of threads that SHAPEIT will use, call shapeit with the number of threads specified by the value $PBS_NUM_PPN:

shapeit --threads $PBS_NUM_PPN other_command_line_arguments


Although the software is free for academic work, the developers request appropriate citations as described on the SHAPEIT home page.

Running SHAPEIT on Breezy

See the general notes in the introduction above. A precompiled static version of SHAPEIT 2.r790 has been installed as


Example files distributed with the software are available in


Running SHAPEIT on Hermes/Nestor

See the general notes in the introduction above.   Before running SHAPEIT on Hermes, initialize your environment with

module load shapeit

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2015-04-23 - Page created.