
iCallSV: Structural Aberration Detection from NGS datasets
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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

[image: Code Health][image][image][image]

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

  * SGE

  * LSF

* Utilities

  * Running iCallSV on MSK-IMPACT Pools

  * Taking the iCallSV and chechking for processed transcript/cDNA
    in samples

* Submodules

  * iCallSV.iCallSV module

    * iCallSV

  * iCallSV.FilterDellyCalls module

    * FilterDellyCalls

  * iCallSV.Run_Delly module

    * Run_Delly

  * iCallSV.Run_iAnnotateSV module

    * Run_iAnnotate

  * iCallSV.Run_samblaster module

    * Run_samblaster

  * iCallSV.Run_targetSeqView module

    * Run_targetSeqView

  * iCallSV.checkBlackList module

    * checkBlackList

  * iCallSV.checkHotSpotList module

    * checkHotSpotList

  * iCallSV.checkparameters module

    * checkparameters

  * iCallSV.combineVCF module

    * combineVCF

  * iCallSV.dellyVcf2Tab module

    * dellyVcf2Tab

  * iCallSV.dellyVcf2targetSeqView module

    * dellyVcf2targetSeqView

  * iCallSV.filterAnnotatedSV module

    * filterAnnotatedSV

  * iCallSV.utilities.iCallSV_dmp_wrapper module

  * iCallSV.utilities.check_cDNA_contamination module

  * iCallSV.launchThreads module

  * iCallSV.launch_FilterDellyCalls module

    * launch_FilterDellyCalls

  * iCallSV.launch_Run_Delly module

    * launch_Run_Delly

  * iCallSV.make_analysis_dir module

    * make_analysis_dir

  * iCallSV.makebamindex module

    * makebamindex

  * iCallSV.mergeFinalFiles module

    * mergeFinalFiles

  * iCallSV.sortbamByCoordinate module

    * sortbamByCoordinate

  * iCallSV.sortbamByReadName module

    * sortbamByReadName

  * Module contents


Indices and tables
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* Index

* Module Index

* Search Page
