| Author: | Ronak H Shah |
|---|---|
| Contact: | [email protected] |
| Source code: | https://github.com/rhshah/iCallSV |
| Wiki: | http://icallsv.readthedocs.io/en/latest/ |
| License: | Apache License 2.0 |
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.
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.
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:
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 |
This files are given in the data folder inside iCallSV.
| BlackListFile: | (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
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| BlackListGenes: | (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed
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| HotspotFile: | (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
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| GenesToKeep: | (genesToInclude.txt) Gene listed one per line wihout header that are to be kept
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#~~~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: 5python 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 filesNote:
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.
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
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 -vbsub -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"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.> 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