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Texto: Platypus Documentation — Radcliffe Department of Medicine Cookies on this website We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings. Continue Find out more Skip to main content Site Map Accessibility Cookies Contact us Log in Menu Home About us About us Our Divisions Our Clinical Facilities and MRC Units Working at RDM Athena SWAN News Seminars Locations and contact details Research People Study with us Work with us Current vacancies Novo Nordisk - Oxford Fellowships For Staff Contacts, travel and maps Personnel Finance, Grants and Funding Facilities, IT and Health and Safety Graduate Studies Career Development Athena SWAN Communications and public engagement Search Research Lunter Group: Functional Genomics & Machine Learning Lunter Group Platypus Documentation This page contains documentation for the Platypus variant-caller, and is intented to act as a guide for users. Basic instructions for setting up Platypus and running can be found on the main page . Some examples of how to run Platypus can be found here , and a list of frequently asked questions is here . On this page, I will describe the various options that you can set when running Platypus, and the output information which ends up in the VCF and log file. If you think anything is missing, or have any additional questions, please contact andyrimmer@gmail.com. This is a work-in-progress, so apologies for anything not yet covered. Platypus Input Options Platypus has a large number of parameters that can be set from the command-line (run 'python Platypus.py callVariants --help ' for a list, but anything not mentioned here should generally be left alone). The tables below describes all the important command-line options, and tells you what the default value is for each one. Common Variant Calling Options Option Name What Does It Control? Default Value --output, -o Name of the output VCF file AllVariants.vcf --refFile Name of the (indexed) reference FASTA file used for variant calling --bamFiles List of BAM files for calling. Can be comma-separated list, or the name of a text file with one BAM name per line. --regions List of regions in which to identify variants, or a text file containing one region per line. All regions (from BAM header) --assemble Whether to use the assembler to generate candidate haplotypes 0 --source Name of any input VCF(s) to be used for genotyping --nCPU Number of processors/cores to use when running Platypus 1 --logFileName Name of the log file log.txt --bufferSize Size of genomic region (in bases) to read into memory at any one time. Increasing this increases memory usage and reduces run-time. 100000 --minReads Minimum number of reads required to support a variant, before that variant is considered for calling 2 --maxReads Maximum number of allowed reads in region of 'bufferSize '. Platypus will skip any regions with more reads than this, to avoid memory problems. 5000000 --maxVariants Maximum number of variants allowed in a window (windows are typically around 100bp). Increasing this will slow Platypus down, but may give more accurate calls in very divergent regions. 8 --verbosity Level of information produced in log file. Useful for debugging. 2 --minPosterior --maxSize --minFlank In this section Neural network finds motif determining recombination hotspots Platypus Documentation Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data Examples Of How To Run Platypus Platypus FAQ Stampy The OpEx pipeline CAVA: Clinical Annotation of Variants LGENU DECoN: Detection of Exon Copy Number All Platypus and Stampy versions © 2020 Radcliffe Department of Medicine Freedom of Information Privacy Policy Copyright Statement Accessibility Statement About us Our Divisions Investigative Medicine Division Nuffield Division of Clinical Laboratory Sciences Oxford Centre for Diabetes, Endocrinology and Metabolism Division of Cardiovascular Medicine MRC Weatherall Institute of Molecular Medicine MRC Weatherall Institute of Molecular Medicine Our Clinical Facilities and MRC Units Acute Vascular Imaging Centre Cardiovascular Clinical Research Facility Oxford Centre for Clinical Magnetic Resonance Research Working at RDM Equal career opportunities and flexible working Career development and training Athena SWAN News Seminars Locations and contact details Research Cardiovascular Science Haematology and Pathology Diabetes, Metabolism and Endocrinology Cancer Biology Immunology and Infection Stem Cells and Developmental Biology Geratology Experimental Therapeutics Ashrafian Group: Experimental Therapeutics and Clinical Pharmacology Mahmod group Tyler Group Lunter Group: Functional Genomics & Machine Learning Lunter Group People Moustafa Abdalla Ines Abdesselam Adib Abdullah Amanda Adler Satish Adwani Devika Agarwal Olorunsola Agbaje Doaa Ahmed Jila Ajeian Nadia Akawi Naveed Akbar Nasren Akhtar Ioannis Akoumianakis Merve Aksoz Marta Perez Alcantara Yara Alenazi Jack Allen Maryam Alsharqi Sneha Anand Amanda Anderson Agata Antepowicz Charalambos Antoniades Alex Antonopoulos Mahesh Appari Andrew Apps Janhavi Apte Rina Ariga Andrew Armitage Alyssa Armsby Linda Arnold Ritu Arya James Ashford Neil Ashley Nicole Ashman Houman Ashrafian Kate Attfield Christian Babbs Mohsin Badat Ileana Badi Jade Bailey Subita Balaram Abhirup Banerjee Alison Banham Adrian Banning Liliana Barbieri Mike Barnkob Amy Barrett Carole Bataille Matthew Baxter Asha Bayliss Robert Beagrie Daniel Beard John Bell John Bell Elena Benedetto Amanda Bennett Felicity Bennett Nicolas Bery Timothy Betts Ryan Beveridge Shoumo Bhattacharya William Biggs Malenka Bissell Edward Blair Henry Blest Nicholas Blockley Henry Boardman Andrea Borghetto Alessandra Borlotti Jacqueline Boultwood Yavor Bozhilov Adam Braithwaite Robert Brand Matt Brechin Serena Briant Linford Briant Anne Bridgeman Paul Brodersen James Brown Jill Brown Connor Broyles Marella de Bruijn Alastair Buchan Veronica Buckle Paul Buckley Daniel Bulte Martijn van de Bunt Mario Buono Holger Burchert Emma Burke-Smith Oliver Burns Matthew Burrage Shijie Cai David Cain Sarah Califano Ivan Candido-Ferreira Fang Cao Maria Carena Maria Carena Ricardo Carnicer Davide Carone Joana Carrelha Brigid Carter Barbara Casadei Carla Cascone Vincenzo Cerundolo Kuan Cha Hedia Chagraoui Jem Chalk Keith Channon Lise Chauveau Jane Cheeseman Yi-Ling Chen Jili Chen Qian Cheng Amy Chiu Robin Choudhury Constantinos Christodoulides Zoe Christodoulou Sandy Chu Surawee Chuaiphichai Aldo Ciau-Uitz Thomas Clague Sally-Ann Clark Kevin Clark Lynn Clee Liz Cloke Christopher Cole Ruth Coleman Huw Colin-York Michela Colombo Ismael da Conceicao Catriona Conway Daniel Cooke Kerrie Cope Anna Corby Thomas Cornfield Eduardo Calpena Corpas Yvonne Couch Mark Crabtree Fay Croft Heidi Crook Eloise Cross Nicholas Crump Andres Hueso Cuervo Melinda Czéh Liangti Dai Andrea van Dam Rinita Dam Matt Daniels Lorna Daniels Carol Davey James Davies Graham Davies Simon Davis James Dean Rebecca Dean Atanasiu Stefan Demian Niall Dempster Louise Dennis Timothy Dent Geoffrey Denwood Michael Desborough Veronica Alcolea Devesa Matthew Dickinson Marina Diotallevi Tomasz Dobrzycki Cameron Dockerill Michael Dodd Kathleen Dolan Hamid Dolatshad Robert Friedrich Donat Tao Dong Patricia Douglas Gillian Douglas Damien Downes Hal Drakesmith Roy Drissen Edward Drydale Yue Du Claire Duff Sam Dunkley Pamela Dyson James Early James Eaton Carol Eaton Laurienne Edgar Christian Eggeling Mehroz Ehsan Jane Ellis Hanif Esmail Lise Estcourt Rachel Etherington Mark Evans Tracey Evans Martyn Ezra Anne Farmer Martin Farrall Martin Fellermeyer Candida Fenton David Ferguson João Ferreira Fernandes Vanessa Ferreira Lucy Field Alison Fletcher Gary Ford Nicholas Fordham Helena Francis John Frankland Rachel Franklin Joe Frost Xiaopeng Fu Lars Fugger Lars Fugger Tudor Fulga Kezia Gaitskell Parag Gajendragadkar Silvia Galiani Toby Gamlen Jonathan Gamwell Wei Gan Wei Gan Syed Gardezi


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253 www.rdm.ox.ac.uk/people/niall-dempster
254 www.rdm.ox.ac.uk/people/louise-dennis
255 www.rdm.ox.ac.uk/people/timothy-dent
256 www.rdm.ox.ac.uk/people/geoffrey-denwood
257 www.rdm.ox.ac.uk/people/michael-desborough
258 www.rdm.ox.ac.uk/people/veronica-alcolea-devesa
259 www.rdm.ox.ac.uk/people/matthew-dickinson
260 www.rdm.ox.ac.uk/people/marina-diotallevi
261 www.rdm.ox.ac.uk/people/tomasz-dobrzycki
262 www.rdm.ox.ac.uk/people/cameron-dockerill
263 www.rdm.ox.ac.uk/people/michael-dodd
264 www.rdm.ox.ac.uk/people/kathleen-dolan
265 www.rdm.ox.ac.uk/people/hamid-dolatshad
266 www.rdm.ox.ac.uk/people/robert-friedrich-donat
267 www.rdm.ox.ac.uk/people/tao-dong
268 www.rdm.ox.ac.uk/people/patricia-douglas
269 www.rdm.ox.ac.uk/people/gillian-douglas
270 www.rdm.ox.ac.uk/people/damien-downes
271 www.rdm.ox.ac.uk/people/alexander-drakesmith
272 www.rdm.ox.ac.uk/people/roy-drissen
273 www.rdm.ox.ac.uk/people/edward-drydale
274 www.rdm.ox.ac.uk/people/yue-du
275 www.rdm.ox.ac.uk/people/claire-duff
276 www.rdm.ox.ac.uk/people/samuel-dunkley
277 www.rdm.ox.ac.uk/people/pamela-dyson
278 www.rdm.ox.ac.uk/people/james-early
279 www.rdm.ox.ac.uk/people/james-eaton
280 www.rdm.ox.ac.uk/people/carol-eaton
281 www.rdm.ox.ac.uk/people/laurienne-gardner
282 www.rdm.ox.ac.uk/people/christian-eggeling
283 www.rdm.ox.ac.uk/people/mehroz-ehsan
284 www.rdm.ox.ac.uk/people/jane-ellis
285 www.rdm.ox.ac.uk/people/hanif-esmail
286 www.rdm.ox.ac.uk/people/lise-estcourt
287 www.rdm.ox.ac.uk/people/rachel-etherington
288 www.rdm.ox.ac.uk/people/mark-evans
289 www.rdm.ox.ac.uk/people/tracey-evans
290 www.rdm.ox.ac.uk/people/martyn-ezra
291 www.rdm.ox.ac.uk/people/anne-farmer
292 www.rdm.ox.ac.uk/people/martin-farrall
293 www.rdm.ox.ac.uk/people/martin-fellermeyer
294 www.rdm.ox.ac.uk/people/candida-fenton
295 www.rdm.ox.ac.uk/people/david-ferguson
296 www.rdm.ox.ac.uk/people/joao-ferreira-fernandes
297 www.rdm.ox.ac.uk/people/vanessa-ferreira
298 www.rdm.ox.ac.uk/people/lucy-field
299 www.rdm.ox.ac.uk/people/alison-fletcher
300 www.rdm.ox.ac.uk/people/gary-ford
301 www.rdm.ox.ac.uk/people/nicholas-fordham
302 www.rdm.ox.ac.uk/people/helena-francis
303 www.rdm.ox.ac.uk/people/john-frankland
304 www.rdm.ox.ac.uk/people/rachel-franklin
305 www.rdm.ox.ac.uk/people/joe-frost
306 www.rdm.ox.ac.uk/people/xiaopeng-fu
307 www.rdm.ox.ac.uk/people/lars-fugger
308 www.rdm.ox.ac.uk/people/lars-fugger-1
309 www.rdm.ox.ac.uk/people/tudor-fulga
310 www.rdm.ox.ac.uk/people/kezia-gaitskell
311 www.rdm.ox.ac.uk/people/parag-gajendragadkar-1
312 www.rdm.ox.ac.uk/people/silvia-galiani
313 www.rdm.ox.ac.uk/people/toby-gamlen-1
314 www.rdm.ox.ac.uk/people/jonathan-gamwell
315 www.rdm.ox.ac.uk/people/wei-gan
316 www.rdm.ox.ac.uk/people/weigan
317 www.rdm.ox.ac.uk/people/syed-gardezi



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