The variant call format and VCFtools. - Petr Danecek; Adam Auton; Gonçalo R. Abecasis; Cornelis A. Albers; Eric Banks; Mark A. DePristo; Robert E. Handsaker; Gerton Lunter; Gabor T. Marth; Stephen T. Sherry; Gilean McVean; Richard Durbin (Bioinform., 2011)

HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes. - Alexander T. Dilthey; Loukas Moutsianas; Stephen Leslie; Gil McVean (Bioinform., 2011)

High-throughput microbial population genomics using the Cortex variation assembler. - Zamin Iqbal; Isaac Turner; Gil McVean (Bioinform., 2013)

Multi-Population Classical HLA Type Imputation. - Alexander T. Dilthey; Stephen Leslie; Loukas Moutsianas; Judong Shen; Charles Cox; Matthew R. Nelson; Gil McVean (PLoS Comput. Biol., 2013)

A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference. - Sorina Maciuca; Carlos del Ojo Elias; Gil McVean; Zamin Iqbal (WABI, 2016)

Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes. - Luke Jostins; Gilean McVean (Bioinform., 2016)

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs. - Alexander T. Dilthey; Pierre-Antoine Gourraud; Alexander J. Mentzer; Nezih Cereb; Zamin Iqbal; Gil McVean (PLoS Comput. Biol., 2016)

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. - Jerome Kelleher; Alison M. Etheridge; Gilean McVean (PLoS Comput. Biol., 2016)

Integrating long-range connectivity information into de Bruijn graphs. - Isaac Turner; Kiran V. Garimella; Zamin Iqbal; Gil McVean (Bioinform., 2018)

Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. - Sha Joe Zhu; Jacob Almagro-Garcia; Gil McVean (Bioinform., 2018)

HLA*LA - HLA typing from linearly projected graph alignments. - Alexander T. Dilthey; Alexander J. Mentzer; Raphael Carapito; Clare Cutland; Nezih Cereb; Shabir A Madhi; Arang Rhie; Sergey Koren; Seiamak Bahram; Gil McVean; Adam M. Phillippy (Bioinform., 2019)

Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria. - Jason A. Hendry; Dominic Kwiatkowski; Gil McVean (PLoS Comput. Biol., 2021)