{"repo":"oicr-gsi/sequenza","free":true,"listed":false,"github":"https://github.com/oicr-gsi/sequenza","clone":"git clone https://github.com/oicr-gsi/sequenza.git","description":"Workflow for Sequenza, cellularity and ploidy","language":"R","stars":28,"topics":["rnaseq","copy-number-variation","cnv","cnv-detection","cnv-analysis","workflow"],"license":null,"category":"workflow-automation","readme_excerpt":"sequenza Sequenza workflow, Given a pair of cellularity and ploidy parameters, the function returns the most likely allele-specific copy numbers with the corresponding log-posterior probability of the fit, for given values of B-allele frequency and depth ratio. Sequenza workflow, Given a pair of cellularity and ploidy parameters, the function returns the most likely allele-specific copy numbers with the corresponding log-posterior probability of the fit, for given values of B-allele frequency and depth ratio. Overview Overview Dependencies sequenza 2.1.2m sequenza-scripts 2.1.5m sequenza-res 2.1.2 Usage Cromwell Inputs Required workflow parameters: Parameter Value Description --- --- --- snpFile File File (data file with CNV calls from Varscan). cnvFile File File (data file with SNV calls from Varscan). reference String Version of genome reference Optional workflow parameters: Parameter Value Default Description --- --- --- --- gammaRange Array[String] [\"50\", \"100\", \"200\", \"300\", \"400\", \"500\", \"600\", \"700\", \"800\", \"900\", \"1000\", \"1250\", \"1500\", \"2000\"] List of gamma parameters for tuning Sequenza seqmentation step, used by copynumber package. outputFileNamePrefix String \"\" Output prefix to prefix output file names with. Optional task parameters: Parameter Value Default Description --- --- --- --- preprocessInputs.rScript String \"$RSTATS ROOT/bin/Rscript\" path to Rscript preprocessInputs.preprocessScript String \"$SEQUENZA SCRIPTS ROOT/bin/SequenzaPreProcess v2.2.R\" Path to the","default_branch":null,"files":null,"tree":[],"storefront":"/r/oicr-gsi","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/oicr-gsi/sequenza/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}