iCallSV: Structural Aberration Detection from NGS datasets¶
Author: | Ronak H Shah |
---|---|
Contact: | rons.shah@gmail.com |
Source code: | http://github.com/rhshah/iCallSV |
Wiki: | http://icallsv.readthedocs.io/en/latest/ |
License: | Apache License 2.0 |
iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina.
Citation¶
We are in the process of publishing a manuscript describing iCallSV as part of the Structural Variant Detection framework. If you use this software in a publication, for now, please cite our website iCallSV.
Contents:
- iCallSV: Structural Aberration Detection from NGS datasets
- Note
- Required Packages
- Required Data Files
- Configuration File Format
- Quick Usage
- Running on SGE or LSF
- Utilities
- Submodules
- iCallSV.iCallSV module
- iCallSV.FilterDellyCalls module
- iCallSV.Run_Delly module
- iCallSV.Run_iAnnotateSV module
- iCallSV.Run_samblaster module
- iCallSV.Run_targetSeqView module
- iCallSV.checkBlackList module
- iCallSV.checkHotSpotList module
- iCallSV.checkparameters module
- iCallSV.combineVCF module
- iCallSV.dellyVcf2Tab module
- iCallSV.dellyVcf2targetSeqView module
- iCallSV.filterAnnotatedSV module
- iCallSV.utilities.iCallSV_dmp_wrapper module
- iCallSV.utilities.check_cDNA_contamination module
- iCallSV.launchThreads module
- iCallSV.launch_FilterDellyCalls module
- iCallSV.launch_Run_Delly module
- iCallSV.make_analysis_dir module
- iCallSV.makebamindex module
- iCallSV.mergeFinalFiles module
- iCallSV.sortbamByCoordinate module
- iCallSV.sortbamByReadName module
- Module contents