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:
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:
|
||
---|---|---|---|
BlackListGenes: | (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed
|
||
HotspotFile: | (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
|
||
GenesToKeep: | (genesToInclude.txt) Gene listed one per line wihout header that are to be kept
|
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: |
|
license: | Apache License 2.0 |
contact: |
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¶
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.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.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.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 iAnnotateSVParameters: - 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 targetSeqViewParameters: - 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.
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
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.makebamindex module¶
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