Print 'Initializing Gibbs sampler' solver = GeckSolverGibbs() append( '././geck')įrom data import GeckData from solverGibbs import GeckSolverGibbs from postprocess import GeckResults tool_names = ĭata_file = './example_input.txt' print 'Loading data' data = GeckData() To test the main functionality of geck, run gibbs_example.py This project requires Python 2.7 or 3.6, and numpy, scipy, pysam. Seven Bridges also offers a commercial license for GECK. The GPL v3 is an open-source license that guarantees the freedom to share and change the software, and to make sure it remains free software for all its users. GECK is available under the GNU General Public License v3. See pre-print "geck: trio-based comparative benchmarking of variant calls" by P. geck performs the steps marked by (b) and (c). ![]() The image below illustrates the data processing pipeline involved. Geck requires a joint histogram of genotype trio calls as input, and it fits a statistical mixture model and estimates the posterior distributions of genotype confusion matrices and benchmarking metrics: precision, recall, F-score. Genotype Error Comparator Kit is implemented as a python package geck, which estimates and compares the accuracies of two genotyping methods using only their joint result on a family trio.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |