All tools|
ChromoPainter is a package designed for finding and visualising haplotypes in sequence data. fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. URL: http://www.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html Email: hellenth@stats.ox.ac.uk Email: myers@stats.ox.ac.uk Email: dan.lawson@bristol.ac.uk |
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Dr Simon Myers Dr Garrett Hellenthal
Dr Daniel Falush |
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Cortex is a package designed for genome assembly, variant discovery and genotyping analysis on sequence data. URL: http://cortexassembler.sourceforge.net/ Email: zam@well.ox.ac.uk |
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Dr Zamin Iqbal |
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The Genomic Recurrent Event ViEwer (GREVE) software tool creates genome wide or per chromosome plots and summaries of a user generated list of events, typically Copy Number Variations (CNVs), and genes. URL: http://www.well.ox.ac.uk/GREVE/ Email: jcazier@well.ox.ac.uk |
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Dr Jean-Baptiste Cazier |
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GWAMA (Genome-Wide Association Meta Analysis) is a software tool designed to perform meta-analysis of the results of Genome-wide association (GWA) studies of binary or quantitative phenotypes in order to identify signals of association. URL: http://www.well.ox.ac.uk/gwama/ Email: reedik@well.ox.ac.uk Email: amorris@well.ox.ac.uk |
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Dr Reedik Magi Dr Andrew Morris |
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HAPPY is designed to map Quantitative Trait Loci (QTL) in outbred populations descended from crosses between inbred lines. URL: http://www.well.ox.ac.uk/happy/intro.shtml Email: richard.mott@well.ox.ac.uk |
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Prof Richard Mott |
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LDhat is a package for analysing patterns of linkage disequilibrium and estimating recombination rates from population genetic data. URL: http://ldhat.sourceforge.net/ Email: adam.auton@einstein.yu.edu |
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Dr Adam Auton Prof Gil McVean |
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A suite of software tools written to facilitate the analysis of genome-wide association studies including IMPUTE and SNPTEST. URL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html Email: marchini@stats.ox.ac.uk |
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Dr Jonathon Marchini |
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OncoSNP is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. URL: https://sites.google.com/site/oncosnp/home Email: c.yau@imperial.ac.uk Email: cholmes@stats.ox.ac.uk |
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Dr Chris Yau Dr Chris Holmes |
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Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. URL: http://www.well.ox.ac.uk/platypus Email: rimmer@well.ox.ac.uk |
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Dr Andrew Rimmer Iain Mathieson Dr Gerton Lunter |
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QuantiSNP is an analytical tool for the analysis of copy number variation using whole genome SNP genotyping data. URL: http://www.well.ox.ac.uk/quantisnp/ Email: c.yau@imperial.ac.uk Email: cholmes@stats.ox.ac.uk Email: ragoussis.PA@well.ox.ac.uk |
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Dr Chris Yau Dr Chris Holmes Dr Jiannis Ragoussis |
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Stampy is a powerfull tool designed for ultra sensitive and specific mapping of short read sequences onto a reference genome. URL: http://www.well.ox.ac.uk/project-stampy Email: gerton.lunter@well.ox.ac.uk |
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Dr Gerton Lunter |
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VCFtools is a program designed for manipulating vcf files generated by variant callers. URL: http://vcftools.sourceforge.net/ Email: adam.auton@einstein.yu.edu |
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Dr Adam Auton |
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