iCallSV: Structural Aberration Detection from NGS datasets

Note

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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

#~~~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

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
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

SGE

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

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

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

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

iCallSV

Description:

iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina

author:

Ronak H Shah

copyright:
  1. 2016-2017 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
license:

Apache License 2.0

contact:

rons.shah@gmail.com

iCallSV.FilterDellyCalls module

FilterDellyCalls

Description:This module will filter calls made by Delly which are in a VCF format
iCallSV.FilterDellyCalls.GetCaseFlag(caseDR, caseDV, preciseFlag, caseRR, caseRV, caseAltFreq, caseTotalCount)[source]

This will check if the case sample passes or not

Parameters:
  • caseDR (int) – int representing number of reference reads for case reported by delly
  • caseDV (int) – int representing number of variant reads for case reported by delly
  • preciseFlag (str) – str representing if an event is precise or imprecise
  • caseRR (int) – int representing number of split reference reads for case reported by delly
  • caseRV (int) – int representing number of split variant reads for case reported by delly
  • caseAltFreq (float) – float representing altratio threshold for case
  • caseTotalCount (int) – int repeseting readcount threshold for case
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.FilterDellyCalls.GetControlFlag(controlDR, controlDV, preciseFlag, controlRR, controlRV, controlAltFreq)[source]

This will check if the control sample passes or not

Parameters:
  • controlDR (int) – int representing number of reference reads for control reported by delly
  • controlDV (int) – int representing number of variant reads for control reported by delly
  • preciseFlag (str) – str representing if an event is precise or imprecise
  • controlRR (int) – int representing number of split reference reads for control reported by delly
  • controlRV (int) – int representing number of split variant reads for control reported by delly
  • controlAltFreq (float) – float representing altratio threshold for control
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.FilterDellyCalls.GetFilteredRecords(dellyVarialbles, thresholdVariables, hotspotDict, blacklist)[source]

This will Filter one record at a time

Parameters:
  • dellyVariables (str) – str having all delly variables separated by ”,”
  • thresholdVariables (str) – str having all delly threshold variables separated by ”,”
  • hotspotDict (dict) – A dict containing hotspot regions
  • blacklist (list) – A list containing blacklist regions
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.FilterDellyCalls.run(inputVcf, outputDir, controlId, caseID, hotspotFile, blacklistFile, svlength, mapq, mapqHotspot, caseAltFreqHotspot, caseTotalCountHotspot, controlAltFreqHotspot, caseAltFreq, caseTotalCount, controlAltFreq, peSupport, srSupport, peSupportHotspot, srSupportHotspot, peSupportCase, srSupportCase, peSupportHotspotCase, srSupportHotspotCase, peSupportControl, srSupportControl, peSupportHotspotControl, srSupportHotspotControl, verbose)[source]

``main:``Filter calls made by Delly which are in a VCF format

Parameters:
  • inputVcf (str) – Input VCF file name with path
  • outputDir (str) – Output directory
  • controlId (str) – Control Sample ID (Should be part of Sample Name in VCF)
  • caseID (str) – Case Sample ID (Should be part of Sample Name in VCF)
  • hospotFile (str) – List of Genes that have Hotspot Structural Variants (Tab-delimited Format without header:chr start end geneName).
  • blacklistFile (str) – List of Genes that have blacklist of Structural Variants (Tab-delimited Format without header:chr start1 chr2 start2; where chr1==chr2, end==start2).
  • caseAltFreq (float) – Alternate Allele Frequency threshold for case
  • caseTotalCount (int) – Total ReadCount threshold for case
  • ccontrolAltFreq (flaot) – Alternate Allele Frequency threshold for control
  • peSupport (int) – overall pair-end read support threshold for the event
  • srSupport (int) – overall split-reads support threshold for the event
  • peSupportHotspot (int) – overall pair-end read support threshold for the event in hot-spot region
  • srSupportHotspot (int) – overall split-reads support threshold for the event in hot-spot region
  • peSupportCase (int) – pair-end read support threshold for the event in the Case sample
  • srSupportCase (int) – split-reads support threshold for the event in the Case sample
  • peSupportHotspotCase (int) – pair-end read support threshold for the event in hot-spot region for the Case sample
  • srSupportHotspotCase (int) – split-reads support threshold for the event in hot-spot region for the Case sample
  • peSupportControl (int) – pair-end read support threshold for the event in the Control sample
  • srSupportControl (int) – split-reads support threshold for the event in the Control sample
  • peSupportHotspotControl (int) – pair-end read support threshold for the event in hot-spot region for the Control sample
  • srSupportHotspotControl (int) – split-reads support threshold for the event in hot-spot region for the Control sample
  • svlength (int) – length of the structural variants
  • mapq (int) – overall mapping quality
  • mapqHotspot (int) – mapping quality for hot-spots
Returns:

A str name of filtered vcf file

Return type:

str

iCallSV.Run_Delly module

Run_Delly

Description:Runs the delly program on case and control bam file to give its results
iCallSV.Run_Delly.run(delly, version, bcftools, analysisType, reference, controlBam, caseBam, caseId, mapq, excludeRegions, outputdir, verbose, debug)[source]

This will Runs the delly program on case and control bam file to give its results.

Parameters:
  • delly (str) – Path to delly executables (0.7.3 or above)
  • bcftools (str) – Path to bcftools executables (1.3.1 or above)
  • type (str) – What ot run in delly, DEL:Deletion, DUP: Duplication,TRA:Translocation, INV:Inversion
  • reference (str) – Reference Genome that was used to align the reads.
  • controlBam (str) – Path to control/normal bam file
  • caseBam (str) – Path to case/tumor bam file
  • controlID (str) – Id of the control/normal sample
  • caseID (str) – Id of the case/tumor sample
  • mapq (int) – mapping quality cutoff for delly
  • excludeRegions (str) – Regions to be excluded for calling structural variation.
  • outputdir (str) – directory for the output of delly
  • debug (bool) – If you just wish to test what we will do
Returns:

str of the output vcf

Return type:

str

iCallSV.Run_iAnnotateSV module

Run_iAnnotate

Description:This module will run iAnnotateSV package
iCallSV.Run_iAnnotateSV.run(python, iAnnotateSV, build, distance, canonicalTranscriptFile, uniprotFile, cosmicFile, cosmicCountsFile, repeatregionFile, dgvFile, inputTabFile, outputPrefix, outputDir)[source]

This module will run iAnnotateSV package.

Parameters:
  • python (str) – Location for the python executable.
  • iAnnotateSV (str) – Location of the wrapper iAnnotateSV package (iAnnotateSV.py)
  • build (str) – Which human reference file to be used, hg18,hg19 or hg38
  • inputTabFile (str) – Tab-Delimited Input FIle compatible with iAnnotateSV package.
  • outputPrefix (str) – Prefix of the output files/DIR with Annotations and images
  • outputDir (str) – Name of the output directory where the outputPrefix will be written
  • uniprotFile (str) – Location for ucsc uniprot file
  • cosmicFile (str) – Location for cosmic census file
  • cosmicCountsFile (str) – Location for cosmic fusion counts file
  • repeatregionFile (str) – Location for repeat region file
  • dgvFile (str) – Location for database of Genomic Variants file
Returns:

str of the output file

Return type:

str

iCallSV.Run_samblaster module

Run_samblaster

Description:This module will run samblaster for extracting discordant and spit reads in sam format
iCallSV.Run_samblaster.run(samtools, samblaster, bamFile, discordantFileName, splitFileName, outputDir)[source]

iCallSV.Run_targetSeqView module

Run_targetSeqView

Description:This module will run targetSeqView
iCallSV.Run_targetSeqView.run(RLocation, targetSeqView, nodes, bamFilePath, svFile, build, readLength, outputDir, outsvFileName)[source]

This module will run targetSeqView.

Parameters:
  • RLocation (str) – Location of the R executable (>3.1.2).
  • targetSeqView (str) – Location of R script that will run tragetSeqView
  • nodes (int) – Number of parallel nodes for running targetSeqView
  • bamFile (str) – Location of the bamFile which has the structural variant events.
  • svFile (str) – targetSeqView compatible input structural variant file.
  • build (str) – Which human reference file to be used, hg18,hg19 or hg38
  • readLength (int) – Sequencing Read Length (101)
  • outputDir (str) – Directory for output files
  • outsvFile (str) – Name of the output structural variant file that has added confidence score to it.
Returns:

str of the output file

Return type:

str

iCallSV.checkBlackList module

checkBlackList

Description:This module will read the Black List file and tell if and event is blacklisted or not
iCallSV.checkBlackList.CheckIfItIsBlacklisted(chr1, start1, chr2, start2, blacklist, extention)[source]

Check if coordinate are present in the blacklist region file

Parameters:
  • chr1 (str) – str of the breakpoint in first chromosome
  • start1 (int) – int of the start location of the breakpoint in first chromosome
  • chr2 (str) – str of the breakpoint in second chromosome
  • start2 (int) – int of the start location of the breakpoint in second chromosome
  • blacklist (list) – A list containing black listed regions
  • extension (int) – an value for search in positive and negative direction of the start1 and start2 location
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.checkBlackList.ReadBlackListFile(BlackListFile)[source]

Read the blacklist region file

Parameters:BlackListFile (str) – str of file to be read.
Returns:A list containing black listed regions.
Return type:list.

iCallSV.checkHotSpotList module

checkHotSpotList

Description:This module will read the hotspot file and tell if it is a hotspot or not
iCallSV.checkHotSpotList.CheckIfItIsHotspot(chr1, start1, chr2, start2, hotspotDict)[source]

Check if coordinate are present in the hotspot region file

Parameters:
  • chr1 (str) – str of the breakpoint in first chromosome
  • start1 (int) – int of the start location of the breakpoint in first chromosome
  • chr2 (str) – str of the breakpoint in second chromosome
  • start2 (int) – int of the start location of the breakpoint in second chromosome
  • hotspotDict (dict) – A dict containing hotspot regions
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.checkHotSpotList.ReadHotSpotFile(HotSpotFile)[source]

Read the HotSpot region file

Parameters:HotSpotFile (str) – str of file to be read.
Returns:A dict containing hotspot regions
Return type:dict

iCallSV.checkparameters module

checkparameters

Description:This modules checks the parameters for various type of inputs.
iCallSV.checkparameters.checkDellyAnalysisType(varaibleToCheck)[source]

Check if the variable for Delly analysis exists or not`

Parameters:variableToCheck (str) – check if str is DEL|DUP|INV|TRA
Returns:None
Return type:None
iCallSV.checkparameters.checkDir(folderToCheck)[source]

Check if the folder exists or not`

str.

Parameters:folderToCheck (str) – Name of the folder to be checked.
Returns:None
Return type:None
iCallSV.checkparameters.checkEmpty(variableToCheck, variableName)[source]

Check if the variable is None or not`

Parameters:
  • variableToCheck (str) – check if str is None or not
  • variableName (str) – Name of the None object to be verified
Returns:

None

Return type:

None

iCallSV.checkparameters.checkFile(fileToCheck)[source]

Check if the file exists or not`

Parameters:fileToCheck (str) – Name of the file to be checked.
Returns:None
Return type:None
iCallSV.checkparameters.checkInt(variableToCheck, variableName)[source]

Check if the variable is int or not`

Parameters:
  • variableToCheck (int) – Check if it is int or not
  • variableName (str) – Name of the int object to be verified
Returns:

None

Return type:

None

iCallSV.combineVCF module

combineVCF

Description:This module will combine multiple vcf file with same headers
iCallSV.combineVCF.run(vcfFiles, combinedVCF, verbose)[source]

This will combine multiple vcf file with same headers

Parameters:
  • vcfFiles (list) – a list of .vcf files to be combined
  • combinedVCF (str) – str for the output of combined vcf files
  • verbose (bool) – a boolean
Returns:

A str name of combined vcf file

Return type:

str

iCallSV.dellyVcf2Tab module

dellyVcf2Tab

Description:This module converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV
iCallSV.dellyVcf2Tab.vcf2tab(vcfFile, outputDir, verbose)[source]

This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV

Parameters:
  • vcfFile (str) – str of vcf file to be converted
  • outputDir (str) – str for the output directory
  • verbose (bool) – a boolean
Returns:

A str name of tab-delimited file

Return type:

str

iCallSV.dellyVcf2targetSeqView module

dellyVcf2targetSeqView

Description:Convert VCF to targetSeqView
iCallSV.dellyVcf2targetSeqView.Convert2targetSeqView(sampleName, sampleBamName, sampleSplitBamName, vcfFile, outputDir, outputFileName)[source]

This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to targetSeqView

Parameters:
  • sampleName (str) – str for the name of the sample being analyzed
  • sampleBamName (str) – str for the pair-end reads bam file
  • sampleSplitBamName (str) – str for the split reads bam file
  • vcfFile (str) – str of vcf file to be converted
  • outputDir (str) – str for the output directory
  • outputFileName (str) – str for the output File
Returns:

A str name of tab-delimited file

Return type:

str

iCallSV.filterAnnotatedSV module

filterAnnotatedSV

Description:This module will filter calls from the merged file
iCallSV.filterAnnotatedSV.checkBlackListGene(gene1, gene2, blacklistGenes)[source]

This will check for blacklisted genes

Parameters:
  • gene1 (str) – str for the name of gene at breakpoint 1
  • gene2 (str) – str for the name of gene at breakpoint 2
  • blacklistGenes (list) – list containing blacklisted genes
  • genesToKeepFile (str) – str for the txt file containing genes to keep
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.filterAnnotatedSV.checkEventInIntronFlag(gene1, gene2, site1, site2)[source]

This will Check if the event is in the intron only and not affecting splicing

Parameters:
  • gene1 (str) – str for the name of gene at breakpoint 1
  • gene2 (str) – str for the name of gene at breakpoint 2
  • site1 (str) – str for the description of site in breakpoint 1
  • site2 (str) – str for the description of site in breakpoint 2
Returns:

A boolean tag indicating True or False

Return type:

bool

iCallSV.filterAnnotatedSV.checkGeneListToKeep(gene1, gene2, keepGenes)[source]
iCallSV.filterAnnotatedSV.run(inputTxt, outputDir, outPrefix, blacklistGenesFile, verbose, genesToKeepFile='somefile.txt')[source]

This will filter sv calls from the final merged file.

Parameters:
  • inputTxt (str) – str for the txt file to be filtered
  • outputDir (str) – str for the output directory
  • outputPrefix (str) – str prefix for the output File
  • blacklistGenesFile (str) – str for the txt file containing blacklisted genes
  • verbose (bool) – a boolean
  • genesToKeepFile (str) – str for the txt file containing genes to keep
Returns:

A str name of final sv file

Return type:

str

iCallSV.utilities.iCallSV_dmp_wrapper module

iCallSV.utilities.check_cDNA_contamination module

iCallSV.launchThreads module

Created on December 21, 2015 Description: This module will be launching functions as threads @author: Ronak H Shah

class iCallSV.launchThreads.myThread(threadID, name, counter)[source]

Bases: threading.Thread

run()[source]
iCallSV.launchThreads.print_time(threadName, delay, counter)[source]

iCallSV.launch_FilterDellyCalls module

launch_FilterDellyCalls

Description:This module will filter delly results and create filtered delly vcf files
iCallSV.launch_FilterDellyCalls.launch_filterdellycalls_for_different_analysis_type(args, config, sampleOutdirForDelly, del_vcf, dup_vcf, inv_vcf, tra_vcf)[source]

This will launch the filtering of delly calls in parallel.

Parameters:
  • args (Namespace) – Namespace of args to get other variables
  • config (Namespace) – configuration file passed to iCallSV
  • sampleOutdirForDelly (str) – Output directory for delly vcf files.
  • del_vcf (str) – Path to deletion based vcf file
  • dup_vcf (str) – Path to duplication based vcf file
  • inv_vcf (str) – Path to inversion based vcf file
  • tra_vcf (str) – Path to translocation based vcf file
Returns:

Multiple objects

Return type:

list

iCallSV.launch_Run_Delly module

launch_Run_Delly

Description:This module will be launching delly using Run_Delly
iCallSV.launch_Run_Delly.launch_delly_for_different_analysis_type(args, config, sampleOutdirForDelly)[source]

This will launch delly calls in parallel.

Parameters:
  • args (Namespace) – Namespace of args to get other variables
  • config (Namespace) – configuration file passed to iCallSV
  • sampleOutdirForDelly (str) – Output directory for delly vcf files.
Returns:

Multiple objects

Return type:

list

iCallSV.make_analysis_dir module

make_analysis_dir

Description:This module will make directory structure for running analysis
iCallSV.make_analysis_dir.makeOutputDir(args, tool)[source]

This will make the output directory tree.

Parameters:args (Namespace) – Namespace of args to get other variables
Returns:Multiple objects
Return type:list

iCallSV.makebamindex module

makebamindex

Description:Use PySAM to make bam index
iCallSV.makebamindex.MakeIndex(bamFile)[source]

This will make bam index if not there for a bam file using pysam.

Parameters:bamFile (str) – Path to bam file
Returns:None
Return type:None

iCallSV.mergeFinalFiles module

mergeFinalFiles

Description:Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file
iCallSV.mergeFinalFiles.run(aId, bId, vcfFile, annoTab, confTab, outDir, outputPrefix, verbose)[source]

This will Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file

Parameters:
  • aId (str) – Sample ID for case that has the structural abberations
  • bId (str) – Sample ID for control
  • vcfFile (str) – Delly filtered and merged VCF file
  • annoTab (str) – iAnnotateSV tab-delimited file with annotations
  • confTab (str) – targetSeqView tab-delimited file with probability score
  • outputDir (str) – Directory to write the output file
  • outputPrefix (str) – Output File Prefix
Returns:

str of the tab-delimited file

Return type:

str

iCallSV.sortbamByCoordinate module

sortbamByCoordinate

Description:This module will sort bam file by coordinate
iCallSV.sortbamByCoordinate.sortBam(inputBam, outputBamName, outputDir)[source]

iCallSV.sortbamByReadName module

sortbamByReadName

Description:This module will sort bam file by name
iCallSV.sortbamByReadName.sortBam(inputBam, outputBamName, outputDir)[source]

Module contents