iCallSV: Structural Aberration Detection from NGS datasets ================================================================ Note ==== For some reason docstrings is not shown by `Read The Docs `_ So please use these url from `Github `_ with `Html Preview `_ for each module information: `Per Module Info `_ Required Packages ================= We require that you install: :pandas: `v0.16.2 `_ :biopython: `v1.65 `_ :pysam: `v0.8.4 `_ :pyvcf: `0.6.7 `_ :Delly: `v0.7.5 `_ :targetSeqView: `master `_ :iAnnotateSV: `v1.0.6 `_ :coloredlogs: `v5.2 `_ Required Data Files =================== This files are given in the ``data`` folder inside iCallSV. :BlackListFile: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order: **chromosome 1, breakpoint 1, chromosome 2, breakpoint 2** :Example: 7 140498077 5 175998094 :BlackListGenes: (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed :Example: LINC00486 CNOT4 :HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order: **chromosome, start, end, name** :Example: 2 29416089 30143525 ALK :GenesToKeep: (genesToInclude.txt) Gene listed one per line wihout header that are to be kept :Example: ALK BRAF Configuration File Format ========================= .. code-block:: sh #~~~Template configuration file to run iCallSV~~~# #### Path to python executable ### [Python] PYTHON: #### Path to R executable and R Lib ### [R] RHOME: RLIB: #### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)### [SVcaller] DELLY: DellyVersion: BCFTOOLS: #### Path to hg19 Referece Fasta file ### [ReferenceFasta] REFFASTA: #### Path to file containing regions to exclude please follow Delly documentation for this ### [ExcludeRegion] EXREGIONS: #### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ### [HotSpotRegions] HotspotFile: GenesToKeep: #### Path to file containing regions/genes to filter ### [BlackListRegions] BlackListFile: BlackListGenes: #### Path to samtools executable ### [SAMTOOLS] SAMTOOLS: #### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ### [iAnnotateSV] ANNOSV: GENOMEBUILD: DISTANCE: CANONICALTRANSCRIPTFILE: UNIPROTFILE: CosmicCensus: CosmicFusionCounts: RepeatRegionAnnotation: DGvAnnotations: #### TargetSeqView Parameters ### [TargetSeqView] CalculateConfidenceScore: GENOMEBUILD: ReadLength: #### Parameters to run Delly ### [ParametersToRunDelly] MAPQ: 20 NumberOfProcessors: 4 [ParametersToFilterDellyResults] ####Case Allele Fraction Hotspot#### CaseAltFreqHotspot: 0.05 ####Total Case Coverage Hotspot##### CaseCoverageHotspot = 5 ####Control Allele Fraction Hotspot#### ControlAltFreqHotspot = 0 ####Case Allele Fraction#### CaseAltFreq: 0.10 ####Total Case Coverage##### CaseCoverage = 10 ####Control Allele Fraction#### ControlAltFreq = 0 ###Overall Supporting Read-pairs ### OverallSupportingReads: 5 ###Overall Supporting Read-pairs Hotspot ### OverallSupportingReadsHotspot: 3 ###Overall Supporting splitreads ### OverallSupportingSplitReads: 0 ###Overall Supporting splitreads Hotspot ### OverallSupportingSplitReadsHotspot: 0 ###Case Supporting Read-pairs ### CaseSupportingReads: 2 ###Case Supporting splitreads ### CaseSupportingSplitReads: 0 ###Case Supporting Read-pairs Hotspot ### CaseSupportingReadsHotspot: 1 ###Case Supporting splitreads Hotspot ### CaseSupportingSplitReadsHotspot: 0 ###Control Supporting Read-pairs ### ControlSupportingReads: 3 ###Control Supporting Read-pairs Hotspot ### ControlSupportingReadsHotspot: 3 ###Control Supporting splitreads ### ControlSupportingSplitReads: 3 ###Control Supporting splitreads Hotspot ### ControlSupportingSplitReadsHotspot: 3 ###Length of Structural Variant### LengthOfSV: 500 ###Overall Mapping Quality Threshold### OverallMapq: 20 ###Overall Mapping Quality Threshold Hotspot### OverallMapqHotspot: 5 Quick Usage =========== .. code-block:: sh python iCallSV.py -sc /path/to/template.ini -abam /path/to/casebamFile -bbam /path/to/controlbamFile -aId caseID -bId controlId -o /path/to/output/directory -op prefix_for_the_output_files .. code-block:: sh python iCallSV.py -h usage: iCallSV.py [-h] [-v] [-V] -sc config.ini -abam caseBAMFile.bam -bbam controlBAMFile.bam -aId caseID -bId controlID -o /somepath/output -op TumorID iCallSV.iCallSV -- wrapper to run iCallSV package Created by Ronak H Shah on 2015-03-30. Copyright 2015-2016 Ronak H Shah. All rights reserved. Licensed under the Apache License 2.0 http://www.apache.org/licenses/LICENSE-2.0 Distributed on an "AS IS" basis without warranties or conditions of any kind, either express or implied. USAGE optional arguments: -h, --help show this help message and exit -v, --verbose set verbosity level [default: True] -V, --version show program's version number and exit -sc config.ini, --svConfig config.ini Full path to the structural variant configuration -abam caseBAMFile.bam, --caseBam caseBAMFile.bam Full path to the case bam file -bbam controlBAMFile.bam, --controlBam controlBAMFile.bam Full path to the control bam file -aId caseID, --caseId caseID Id of the case to be analyzed, this will be the sub- folder -bId controlID, --controlId controlID Id of the control to be used, this will be used for filtering variants -o /somepath/output, --outDir /somepath/output Full Path to the output dir. -op TumorID, --outPrefix TumorID Id of the Tumor bam file which will be used as the prefix for output files Running on SGE or LSF ===================== .. sidebar:: Note: For both SGE and LSF you need to provide total number of cores based on the number of threads you have assinged to delly installation using **OMP_NUM_THREADS**. .. sidebar:: Note: For example: if you set **OMP_NUM_THREADS** as `export OMP_NUM_THREADS=3` then you need to set total number of cores to be 13 (12 + 1 extra as buffer) so for each of the Delly program it utilizes 3 cores. Here I use pythons multiprocessing module to launch delly, so all four programs would be launch as seprate process utilizing number of threads given to them but setting the **OMP_NUM_THREADS** SGE --- .. code-block:: sh qsub -q some.q -N iCallSV_JobName -o iCallSV.stdout -e iCallSV.stderr -V -l h_vmem=6G,virtual_free=6G -pe smp 13 -wd /some/path/to/working/dir -sync y -b y python iCallSV.py -sc template.ini -bbam control.bam -abam case.bam -aId caseID -bId controlID -op outputPrefix -o /some/path/to/output/dir -v LSF --- .. code-block:: sh bsub -q some.q -J iCallSV_JobName -o iCallSV.stdout -e iCallSV.stderr -We 24:00 -R "rusage[mem=20]" -M 30 -n 13 -cwd /some/path/to/working/dir "python iCallSV.py -sc template.ini -bbam control.bam -abam case.bam -aId caseID -bId controlID -op outputPrefix -o /some/path/to/output/dir -v" Utilities ========= Running iCallSV on MSK-IMPACT Pools ----------------------------------- **This is only for MSK-IMPACT internal samples** .. code-block:: sh python iCallSV_dmp_wrapper.py -h usage: iCallSV_dmp_wrapper.py [options] Run iCallSV on selected pools using MSK data optional arguments: -h, --help show this help message and exit -fl folders.fof, --folderList folders.fof Full path folders file of files. -qc /some/path/qcLocation, --qcLocation /some/path/qcLocation Full path qc files. -b /some/path/bamlocation, --bamLocation /some/path/bamlocation Full path bam files. -P /somepath/python, --python /somepath/python Full path Pyhton executables. -icsv /somepath/iCallSV.py, --iCallSV /somepath/iCallSV.py Full path iCallSV.py executables. -conf /somepath/template.ini, --iCallSVconf /somepath/template.ini Full path configuration file to run iCallSV -q all.q or clin.q, --queue all.q or clin.q Name of the SGE queue -qsub /somepath/qsub, --qsubPath /somepath/qsub Full Path to the qsub executables of SGE. -t 5, --threads 5 Number of Threads to be used to run iCallSV -v, --verbose make lots of noise [default] -o /somepath/output, --outDir /somepath/output Full Path to the output dir. -of outputfile.txt, --outDir outputfile.txt Name of the final output file. Taking the iCallSV and chechking for processed transcript/cDNA in samples ------------------------------------------------------------------------- .. code-block:: sh python check_cDNA_contamination.py -h usage: check_cDNA_contamination.py [options] Calculate cDNA contamination per sample based of the Structural Variants Pipeline result optional arguments: -h, --help show this help message and exit -v, --verbose make lots of noise [default] -s SVfile.txt, --svFile SVfile.txt Location of the structural variant file to be used -o cDNA_contamination, --outputFileName cDNA_contamination Full path name for the output file Submodules ========== iCallSV.iCallSV module ---------------------- .. automodule:: iCallSV.iCallSV :members: :undoc-members: :show-inheritance: iCallSV.FilterDellyCalls module ------------------------------- .. automodule:: iCallSV.FilterDellyCalls :members: :undoc-members: :show-inheritance: iCallSV.Run_Delly module ------------------------ .. automodule:: iCallSV.Run_Delly :members: :undoc-members: :show-inheritance: iCallSV.Run_iAnnotateSV module ------------------------------ .. automodule:: iCallSV.Run_iAnnotateSV :members: :undoc-members: :show-inheritance: iCallSV.Run_samblaster module ----------------------------- .. automodule:: iCallSV.Run_samblaster :members: :undoc-members: :show-inheritance: iCallSV.Run_targetSeqView module -------------------------------- .. automodule:: iCallSV.Run_targetSeqView :members: :undoc-members: :show-inheritance: iCallSV.checkBlackList module ----------------------------- .. automodule:: iCallSV.checkBlackList :members: :undoc-members: :show-inheritance: iCallSV.checkHotSpotList module ------------------------------- .. automodule:: iCallSV.checkHotSpotList :members: :undoc-members: :show-inheritance: iCallSV.checkparameters module ------------------------------ .. automodule:: iCallSV.checkparameters :members: :undoc-members: :show-inheritance: iCallSV.combineVCF module ------------------------- .. automodule:: iCallSV.combineVCF :members: :undoc-members: :show-inheritance: iCallSV.dellyVcf2Tab module --------------------------- .. automodule:: iCallSV.dellyVcf2Tab :members: :undoc-members: :show-inheritance: iCallSV.dellyVcf2targetSeqView module ------------------------------------- .. automodule:: iCallSV.dellyVcf2targetSeqView :members: :undoc-members: :show-inheritance: iCallSV.filterAnnotatedSV module -------------------------------- .. automodule:: iCallSV.filterAnnotatedSV :members: :undoc-members: :show-inheritance: iCallSV.utilities.iCallSV_dmp_wrapper module -------------------------------------------- .. automodule:: iCallSV.utilities.iCallSV_dmp_wrapper :members: :undoc-members: :show-inheritance: iCallSV.utilities.check_cDNA_contamination module ------------------------------------------------- .. automodule:: iCallSV.utilities.check_cDNA_contamination :members: :undoc-members: :show-inheritance: iCallSV.launchThreads module ---------------------------- .. automodule:: iCallSV.launchThreads :members: :undoc-members: :show-inheritance: iCallSV.launch_FilterDellyCalls module -------------------------------------- .. automodule:: iCallSV.launch_FilterDellyCalls :members: :undoc-members: :show-inheritance: iCallSV.launch_Run_Delly module ------------------------------- .. automodule:: iCallSV.launch_Run_Delly :members: :undoc-members: :show-inheritance: iCallSV.make_analysis_dir module -------------------------------- .. automodule:: iCallSV.make_analysis_dir :members: :undoc-members: :show-inheritance: iCallSV.makebamindex module --------------------------- .. automodule:: iCallSV.makebamindex :members: :undoc-members: :show-inheritance: iCallSV.mergeFinalFiles module ------------------------------ .. automodule:: iCallSV.mergeFinalFiles :members: :undoc-members: :show-inheritance: iCallSV.sortbamByCoordinate module ---------------------------------- .. automodule:: iCallSV.sortbamByCoordinate :members: :undoc-members: :show-inheritance: iCallSV.sortbamByReadName module -------------------------------- .. automodule:: iCallSV.sortbamByReadName :members: :undoc-members: :show-inheritance: Module contents --------------- .. automodule:: iCallSV :members: :undoc-members: :show-inheritance: