Package: iCallSV
iCallSV: Structural Aberration Detection from NGS datasetsAuthor:Ronak H ShahContact:rons.shah@gmail.comSource code:http://github.com/rhshah/iCallSVWiki:http://icallsv.readthedocs.io/en/latest/License:Apache License 2.0iCallSV 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.The filtering process can be observed here:WorkflowCitationWe 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 websiteiCallSV.NoteFor some reason docstrings is not shown byRead The DocsSo please use these url fromGithubwithHtml Previewfor each module information:Per Module InfoRequired PackagesWe require that you install:pandas:v0.16.2biopython:v1.65pysam:v0.8.4pyvcf:0.6.7Delly:v0.7.5targetSeqView:masteriAnnotateSV:v1.0.6coloredlogs:v5.2Required Data FilesThis files are given in thedatafolder inside iCallSV.BlackListFile:(blacklist.txt) Tab-delimited file wihout header having black listed regions in order:chromosome 1, breakpoint 1, chromosome 2, breakpoint 2Example:7       140498077       5       175998094BlackListGenes:(blacklistgenes.txt) Gene listed one per line wihout header that are to be removedExample:LINC00486CNOT4HotspotFile:(hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:chromosome, start, end, nameExample:2       29416089        30143525        ALKGenesToKeep:(genesToInclude.txt) Gene listed one per line wihout header that are to be keptExample:ALKBRAFConfiguration File Format#~~~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:20NumberOfProcessors: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:5Quick UsagepythoniCallSV.py-sc/path/to/template.ini-abam/path/to/casebamFile-bbam/path/to/controlbamFile-aIdcaseID-bIdcontrolId-o/path/to/output/directory-opprefix_for_the_output_files>pythoniCallSV.py-husage:iCallSV.py[-h][-v][-V]-scconfig.ini-abamcaseBAMFile.bam-bbamcontrolBAMFile.bam-aIdcaseID-bIdcontrolID-o/somepath/output-opTumorIDiCallSV.iCallSV--wrappertoruniCallSVpackageCreatedbyRonakHShahon2015-03-30.Copyright2015-2016RonakHShah.Allrightsreserved.LicensedundertheApacheLicense2.0http://www.apache.org/licenses/LICENSE-2.0Distributedonan"AS IS"basiswithoutwarrantiesorconditionsofanykind,eitherexpressorimplied.USAGEoptionalarguments:-h,--helpshowthishelpmessageandexit-v,--verbosesetverbositylevel[default:True]-V,--versionshowprogram'sversionnumberandexit-scconfig.ini,--svConfigconfig.iniFullpathtothestructuralvariantconfiguration-abamcaseBAMFile.bam,--caseBamcaseBAMFile.bamFullpathtothecasebamfile-bbamcontrolBAMFile.bam,--controlBamcontrolBAMFile.bamFullpathtothecontrolbamfile-aIdcaseID,--caseIdcaseIDIdofthecasetobeanalyzed,thiswillbethesub-folder-bIdcontrolID,--controlIdcontrolIDIdofthecontroltobeused,thiswillbeusedforfilteringvariants-o/somepath/output,--outDir/somepath/outputFullPathtotheoutputdir.-opTumorID,--outPrefixTumorIDIdoftheTumorbamfilewhichwillbeusedastheprefixforoutputfilesRunning on SGE or LSFNote: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 usingOMP_NUM_THREADS.Note:For example: if you setOMP_NUM_THREADSasexport OMP_NUM_THREADS=3then 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 theOMP_NUM_THREADSSGEqsub-qsome.q-NiCallSV_JobName-oiCallSV.stdout-eiCallSV.stderr-V-lh_vmem=6G,virtual_free=6G-pesmp13-wd/some/path/to/working/dir-syncy-bypythoniCallSV.py-sctemplate.ini-bbamcontrol.bam-abamcase.bam-aIdcaseID-bIdcontrolID-opoutputPrefix-o/some/path/to/output/dir-vLSFbsub-qsome.q-JiCallSV_JobName-oiCallSV.stdout-eiCallSV.stderr-We24:00-R"rusage[mem=20]"-M30-n13-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"UtilitiesRunning iCallSV on MSK-IMPACT PoolsThis is only for MSK-IMPACT internal samples>pythoniCallSV_dmp_wrapper.py-husage:iCallSV_dmp_wrapper.py[options]RuniCallSVonselectedpoolsusingMSKdataoptionalarguments:-h,--helpshowthishelpmessageandexit-flfolders.fof,--folderListfolders.fofFullpathfoldersfileoffiles.-qc/some/path/qcLocation,--qcLocation/some/path/qcLocationFullpathqcfiles.-b/some/path/bamlocation,--bamLocation/some/path/bamlocationFullpathbamfiles.-P/somepath/python,--python/somepath/pythonFullpathPyhtonexecutables.-icsv/somepath/iCallSV.py,--iCallSV/somepath/iCallSV.pyFullpathiCallSV.pyexecutables.-conf/somepath/template.ini,--iCallSVconf/somepath/template.iniFullpathconfigurationfiletoruniCallSV-qall.qorclin.q,--queueall.qorclin.qNameoftheSGEqueue-qsub/somepath/qsub,--qsubPath/somepath/qsubFullPathtotheqsubexecutablesofSGE.-t5,--threads5NumberofThreadstobeusedtoruniCallSV-v,--verbosemakelotsofnoise[default]-o/somepath/output,--outDir/somepath/outputFullPathtotheoutputdir.-ofoutputfile.txt,--outDiroutputfile.txtNameofthefinaloutputfile.Taking the iCallSV and chechking for processed transcript/cDNA in samples>pythoncheck_cDNA_contamination.py-husage:check_cDNA_contamination.py[options]CalculatecDNAcontaminationpersamplebasedoftheStructuralVariantsPipelineresultoptionalarguments:-h,--helpshowthishelpmessageandexit-v,--verbosemakelotsofnoise[default]-sSVfile.txt,--svFileSVfile.txtLocationofthestructuralvariantfiletobeused-ocDNA_contamination,--outputFileNamecDNA_contaminationFullpathnamefortheoutputfile