Genetic Analysis Software

The following programs have been written to facilitate the analysis of genome-wide association studies and other genetic studies.




a program for genotype imputation and phasing in genome-wide association studies and fine-mapping
studies based on a dense set of marker data (such as 1000 Genomes Project haplotypes)

Marchini et al. (2007) Nature Genetics  39 : 906-913,

Howie et al. (2009) PLoS Genetics  5(6): e1000529.

Marchini et al. (2010) Nature Reviews Genetics 11, 499-511

Howie et al. (2011) G3 1(6) 457-470.

Howie et al. (2012) Nature Genetics 44, 955959.


v2.5 (beta)


a program for Frequentist and Bayesian tests of SNP association with binary (case-control) and quantitative phenotypes that takes genotype uncertainty into account.

Marchini et al. (2010) Nature Reviews Genetics 11, 499-511




a program for accurate and efficient phasing of genetic datasets

Delaneau et al. (2012) Nature Methods 9, 179181.
Delaneau et al. (2013) Nature Methods 10, 5-6. [SuppMat]

ASHG 2012 Presentation Thursday, Nov 8 11:00AM

ASHG 2012 Poster 1484 Wed, Nov 7, 3:15-4:15PM



a program that works together with SHAPEIT to produce accurate inference of haplotypes in pedigrees, estimate recombination events and detect genotyping errors.

J. O'Connell, D. Gurdasani, O. Delaneau, et al. (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genetics (in press)




a program to simulate case control datasets at linked SNP markers conditional upon a set of known haplotypes.

Spencer et al. (2009)  PLoS Genetics 5(5).

Su et al. (2011) Bioinformatics 27 (16) 2304-2305.

an R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN and described fully in the paper

Spencer et al. (2009)  PLoS Genetics 5(5)



a program for admixture deconvolution using multiple (i.e. > 2) phased or unphased ancestral panels.

Churchhouse and Marchini (2012) Genet Epidem
DOI: 10.1002/gepi.21692

ASHG 2012 Poster 3384 Thur, Nov 8, 3:15-4:15PM




a program for genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.

Menelaou and Marchini (2012) Bioinformatics doi:10.1093/bioinformatics/bts632.

ASHG 2012 Presentation Thursday, Nov 8 11:15AM




a program to carryout meta-analysis of genetic studies.

Liu et al. (2010)  Nature Genetics 42, 436440.




a program for location and detection of unobserved causal loci in fine-mapping experiments and genome-wide association studies.

Su et al. (2009) Statistical Science 24(4) 430-450.




a joint genotype calling algorithm for array and sequence data. This method can be used to call genotype from just array data.

O'Connell and Marchini (2012) Genet Epi 36: 527537




a genotype calling algorithm for multi-cohort studies.


a program for carrying out SNP and sample quality control (QC) for genome-wide association studies




a program for (a) generating subsets of genotype data, and (b) converting genotype data between the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE.

Contact Information (top)

If you have a question please send a mail to our mail list

You will need to subscribe to the mail list to do this.

IMPORTANT : If you are having a problem with one of the programs please include details of the following when you email.
(a) the version number of the program and the type of computer you are running the program on e.g. SNPTEST v2.1.0 Mac OSX 10.6
(b) include the precise command line(s) you have used
(c) include any log file and/or screen output from the program
(d) sometimes it may be necessary for us to obtain a copy of the data you have so please be prepared to supply this. Otherwise, we may not be able to diagnose the problem.

Licence (top)

Genetics Software Suite, (c) 2007, The University of Oxford (the "Software")
The Software remains the property of the University of Oxford ("the University").

The Genetics Software Suite consists of the software


The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using  the Software.

The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software.
No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. 

You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: quoting reference DP3507.