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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 Site Map Accessibility Cookies Contact us Log in 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 Site Map Accessibility Cookies Contact us Log in 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 Chapman Group: Genome stability and DNA repair mechanisms in cancer and genome diversification 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 Affaf Aliouat 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 Jordan Becker John Bell John Bell Elena Benedetto Amanda Bennett Felicity Bennett 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 Ross Chapman 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 Nicola Curry 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 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 Oliver Featherstone Martin Fellermeyer Candida Fenton David Ferguson João Ferreira Fernandes Vanessa Ferreira Lucy Field Alison Fletcher Gary Ford Nicholas Fordham Helena Francis


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251 www.rdm.ox.ac.uk/people/rinita-dam
252 www.rdm.ox.ac.uk/people/matthew-daniels
253 www.rdm.ox.ac.uk/people/lorna-daniels
254 www.rdm.ox.ac.uk/people/carol-davey
255 www.rdm.ox.ac.uk/people/james-davies
256 www.rdm.ox.ac.uk/people/graham-davies
257 www.rdm.ox.ac.uk/people/simon-davis
258 www.rdm.ox.ac.uk/people/james-dean
259 www.rdm.ox.ac.uk/people/rebecca-dean
260 www.rdm.ox.ac.uk/people/atanasiu-stefan-demian
261 www.rdm.ox.ac.uk/people/niall-dempster
262 www.rdm.ox.ac.uk/people/louise-dennis
263 www.rdm.ox.ac.uk/people/timothy-dent
264 www.rdm.ox.ac.uk/people/geoffrey-denwood
265 www.rdm.ox.ac.uk/people/michael-desborough
266 www.rdm.ox.ac.uk/people/matthew-dickinson
267 www.rdm.ox.ac.uk/people/marina-diotallevi
268 www.rdm.ox.ac.uk/people/tomasz-dobrzycki
269 www.rdm.ox.ac.uk/people/cameron-dockerill
270 www.rdm.ox.ac.uk/people/michael-dodd
271 www.rdm.ox.ac.uk/people/kathleen-dolan
272 www.rdm.ox.ac.uk/people/hamid-dolatshad
273 www.rdm.ox.ac.uk/people/robert-friedrich-donat
274 www.rdm.ox.ac.uk/people/tao-dong
275 www.rdm.ox.ac.uk/people/patricia-douglas
276 www.rdm.ox.ac.uk/people/gillian-douglas
277 www.rdm.ox.ac.uk/people/damien-downes
278 www.rdm.ox.ac.uk/people/alexander-drakesmith
279 www.rdm.ox.ac.uk/people/roy-drissen
280 www.rdm.ox.ac.uk/people/edward-drydale
281 www.rdm.ox.ac.uk/people/yue-du
282 www.rdm.ox.ac.uk/people/claire-duff
283 www.rdm.ox.ac.uk/people/samuel-dunkley
284 www.rdm.ox.ac.uk/people/pamela-dyson
285 www.rdm.ox.ac.uk/people/james-early
286 www.rdm.ox.ac.uk/people/james-eaton
287 www.rdm.ox.ac.uk/people/carol-eaton
288 www.rdm.ox.ac.uk/people/laurienne-gardner
289 www.rdm.ox.ac.uk/people/christian-eggeling
290 www.rdm.ox.ac.uk/people/mehroz-ehsan
291 www.rdm.ox.ac.uk/people/jane-ellis
292 www.rdm.ox.ac.uk/people/hanif-esmail
293 www.rdm.ox.ac.uk/people/lise-estcourt
294 www.rdm.ox.ac.uk/people/rachel-etherington
295 www.rdm.ox.ac.uk/people/mark-evans
296 www.rdm.ox.ac.uk/people/tracey-evans
297 www.rdm.ox.ac.uk/people/martyn-ezra
298 www.rdm.ox.ac.uk/people/anne-farmer
299 www.rdm.ox.ac.uk/people/martin-farrall
300 www.rdm.ox.ac.uk/people/oliver-featherstone
301 www.rdm.ox.ac.uk/people/martin-fellermeyer
302 www.rdm.ox.ac.uk/people/candida-fenton
303 www.rdm.ox.ac.uk/people/david-ferguson
304 www.rdm.ox.ac.uk/people/joao-ferreira-fernandes
305 www.rdm.ox.ac.uk/people/vanessa-ferreira
306 www.rdm.ox.ac.uk/people/lucy-field
307 www.rdm.ox.ac.uk/people/alison-fletcher
308 www.rdm.ox.ac.uk/people/gary-ford
309 www.rdm.ox.ac.uk/people/nicholas-fordham
310 www.rdm.ox.ac.uk/people/helena-francis



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