快速使用
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
在SGE或LSF上运行
注意：
对于sge和lsf，您需要根据已协助使用omp num_threads进行delly安装的线程数提供内核总数。
注意：
例如：如果您将omp num嫒u threads设置为export omp num嫒u threads=3，则需要将总内核数设置为13（12+1额外作为缓冲区），因此对于每个delly程序，它使用3个内核。在这里，我使用pythons多处理模块来启动delly，因此所有四个程序都将作为seprate进程启动，利用给它们的线程数，但设置omp num_threads
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"
实用程序
在msk-impact池上运行icallsv
这仅适用于msk-impact内部示例
> 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.
采集样本中的icallsv和chechking进行转录/cdna处理
> 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
