TY - JOUR T1 - Cpipe: a shared variant detection pipeline designed for diagnostic settings JF - bioRxiv DO - 10.1101/020388 SP - 020388 AU - Simon P Sadedin AU - Harriet Dashnow AU - Paul A James AU - Melanie Bahlo AU - Denis C Bauer AU - Andrew Lonie AU - Sebastian Lunke AU - Ivan Macciocca AU - Jason P Ross AU - Kirby R Siemering AU - Zornitza Stark AU - Susan M White AU - Melbourne Genomics Health Alliance AU - Graham Taylor AU - Clara Gaff AU - Alicia Oshlack AU - Natalie P Thorne Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/06/03/020388.abstract N2 - The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne Genomics Health Alliance, an Australian initiative to promote common approaches to genomics across healthcare institutions. As such, Cpipe has been designed to provide fast, effective and reproducible analysis, while also being highly flexible and customisable to meet the individual needs of diverse clinical settings. Cpipe is being shared with the clinical sequencing community as an open source project and is available at http://cpipeline.org.HIPAAHealth Insurance Portability and Accountability Act1000G1000 Genomes Project [http://1000genomes.org]ExACExome Aggregation Consortium [http://exac.broadinstitute.org]LOVDLeiden Open Variation Database ER -