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Pipeline publication

[…] . Sharma, I. Taylor and I. Westbury for assistance with molecular genetic analysis, and the staff of the OUH NHS Immunology Laboratory for DNA preparation., Accession Codes , The majority of samples studied in WGS500 were consented for clinical investigation only. A small number of samples were collected for general research and WGS data for these samples are available from the ENA under accession number XXX., Competing Financial Interests , All authors at Illumina (see affiliations) are employees of Illumina Inc., a public company that develops and markets systems for genetic analysis. GM, GL and PD are founders and shareholders of Genomics Ltd, a company that develops genome analytics., Stampy read mapper, http://www.well.ox.ac.uk/project-stampy, Platypus variant caller, https://github.com/andyrimmer/Platypus, Picard, www.picard.sourceforge.net, Ensembl regulatory build, http://www.ensembl.org/info/docs/funcgen/regulatory_build.html, NHLBI Exome Variant Server, http://evs.gs.washington.edu/EVS, Copenhagen disease gene association list, http://diseases.jensenlab.org/Search, Eurexpress database, http://discovery.lifemapsc.com/gene-expression-signals/high-throughput/ish-large-scale-dataset-eurexpress, Universal Mutation Database for BRCA2: http://www.umd.be/BRCA2, Each line represents a separate case or family, so if the same gene is reported on two lines, this signifies that the gene is thought to be pathogenic in both cases. Some genes have two mutations in the same affected individual, likely representing com […]

Pipeline specifications

Software tools Stampy, Platypus, Picard
Diseases Genetic Diseases, Inborn