Table of Contents

• Introduction
• Running IMPUTE2 on Breezy
• Running IMPUTE2 on Hermes/Nestor

Introduction

IMPUTE version 2 (IMPUTE2) is a program for inferring haplotypes (phasing) and estimating genotypes (imputing).

This is a serial program and so one should request only a single compute node for IMPUTE2 jobs.  The name of the IMPUTE2 binary executable is impute2.

See the IMPUTE2 Software Versions page (or choose the corresponding tab above) for a list of systems on which the software has been installed.

Running IMPUTE2 on Breezy

See the general notes in the introduction above. A precompiled static version of IMPUTE 2.3.2 has been installed as

/global/software/impute/impute232/bin/impute2

Example files distributed with the software are available in

/global/software/impute/impute232/Example

Running IMPUTE2 on Hermes/Nestor

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

module load impute