Donnelly group

Colin Freeman

Scientific programmer


Wellcome Trust Centre for Human Genetics, Roosevelt Dr.
Oxford, OX3 7BN



+44 (0)1865 287620

Work summary

I am responsible for developing data analysis pipelines and for data management, for various projects including the UKBiobank genotyping project and the Platypus recombination project. Previously, I worked on the WTCCC2 project and prior to that on the HapMap project. I wrote and maintain the GTOOL package which is part of the GWAS suite of software. I provide software tools and support for users on the Donnelly group servers and the 1152 core cluster.

Selected publications

LeishGEN Consortium and Wellcome Trust Case Control Consortium 2. Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. Nat Genet. 2013 Feb;45(2):208-13.
International Stroke Genetics Consortium and Wellcome Trust Case Control Consortium 2. Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke. Nat Genet. 2012 Feb 5;44(3):328-33
International Multiple Sclerosis Genetics Consortium and Wellcome Trust Case Control Consortium 2. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature. 2011 Aug 10;476(7359):214-9.
Myers S, Freeman C, Auton A, Donnelly P, McVean G. A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet. 2008 Sep;40(9):1124-9 
International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61.
International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320.


GTOOL is a program for transforming sets of genotype data for use with the programs from the GWAS suite such as SNPTEST and IMPUTE2.