This is the documentation for using apt-copynumber-wave to compute additional waves from log2 ratios belonging to a set of input CYCHP files. The application can be applied to CN reference (with waves) generated from reference samples coming from CytoScanHD_Array.
The basic requirements for a run of apt-copynumber-wave are:
The output will consist of a modified CN reference with additional wave added to the WaveCorrection data set.
WARNING: apt-copynumber-wave will overwrite any existing output CN Reference file it finds. If you wish to keep existing results make sure to specify a different output directory name.
NOTE: On windows the DOS prompt does not support wildcard expansion and the preferred method is to supply a text file with the path to the cychp files via the '--cychp-files' option (see below for details of file format).
NOTE: The windows DOS prompt also does not allow a continuation of a command with the '\' character, unlike unix. So in the examples shown here the '\' character should be omitted and everything entered on a single line.
apt-copynumber-wave -v 4 \ #verbose output level in the log file ranging from 1 (least details) to 4 (most details)
--cn-reference-input CytoScanHD_Array.na32.v3.REF_MODEL \ #specify the input CN reference that already have at least 1 or more waves and to be augmented from.
--cn-reference-output CytoScanHD_Array.na32.v3.additional6waves.REF_MODEL \ #specify the output CN reference that contain augmented waves
--analysis additional-waves-reference-method.\ #analysis module to compute the additional wave using the input CYCHP files
additional-wave-count=6.\ #number of waves need to be estimated from the input CYCHP files
trim=2.0.\ #trim parameter for absolute adjusted log2 ratios after each wave
percentile=0.75.\ #percentile to use for each probeset in finding wave. E.g., 0.75 means 75-th percentile.
demean=false.\ #true: demean prior to finding each wave; false: otherwise
cn-qc-cutoff=0.35.\ #only includes CYCHP files that have MAPD <= cn-qc-cutoff
selected-qc=snp-qc \ #choose what SNP related QC for filtering input CYCHP files, supported QCs include snp-qc,contrast-qc, contrast-qc-nsp, raw-snp-qc and contrast-qc-rand
snp-qc-cutoff=0.\ #only includes CYCHP files that have the selected SNP related QC >= snp-qc-cutoff
force=false.\ #true: Disable various checks including chip types; false: otherwise.
keep-temp-data=false.\ #true: dump out intermediate data during apt processing; false: otherwise.
use-high-waviness-seg-count=true.\ #true: only includes CYCHP files that have waviness-seg-count > waviness-seg-count-cutoff;false: only includes CYCHP files that have waviness-seg-count <= waviness-seg-count-cutoff
waviness-seg-count-cutoff=0.\ #waviness-seg-count threshold that is used with "use-high-waviness-seg-count" option
--temp-dir mytempDIR \ #specify the directory to hold tempory results
--cychp-files CYCHPFileList.txt #an ASCII file that contains the full path of input cychp files for processing, where the first row of the file is "cychp_files" and each subsequent row corresponds to each cychp file
N/A
apt-copynumber-wave - A program to compute additional copy number waves.
usage:
./apt-copynumber-wave \
--cn-reference-input /CytoFullV2.1-lib/na30.1Gold/Cytogenetics_Array.na30.1.v1.REF_MODEL\
--cn-reference-output /CytoFullV2.1-lib/na30.1Gold/newref/Cytogenetics_Array.na30.1.v1.modified.REF_MODEL\
--analysis additional-waves-reference-method.additional-wave-count=1.trim=2.0\
.percentile=0.75.demean=false.cn-qc-cutoff=0.27.snp-qc-cutoff=1.1.force=false.keep-temp-data=false\
.waviness-seg-count-cutoff=100.use-high-waviness-seg-count=true \
--cychp-files /cychp_files/cychpList.txt\
--temp-dir =/localData/WaveTemp
options:
Common Options (not used by all programs)
-h, --help Display program options and extra
documentation about possible analyses. See
-explain for information about a specific
operation. [default 'false']
-v, --verbose How verbose to be with status messages 0 -
quiet, 1 - usual messages, 2 - more
messages. [default '1']
--console-off Turn off the default messages to the
console but not logging or sockets.
[default 'false']
--use-socket Host and port to print messages over in
localhost:port format [default '']
--version Display version information. [default
'false']
-f, --force Disable various checks including chip
types. Consider using --chip-type option
rather than --force. [default 'false']
--throw-exception Throw an exception rather than calling
exit() on error. Useful for debugging. This
option is intended for command line use
only. If you are wrapping an Engine and
want exceptions thrown, then you should
call Err::setThrowStatus(true) to ensure
that all Err::errAbort() calls result in an
exception. [default 'false']
--analysis-files-path Search path for analysis library files.
Will override AFFX_ANALYSIS_FILES_PATH
environment variable. [default '']
--xml-file Input parameters in XML format (Will
override command line settings). [default
'']
--temp-dir Directory for temporary files when working
off disk. Using network mounted drives is
not advised. When not set, the output
folder will be used. The defaut is
typically the output directory or the
current working directory. [default '']
-o, --out-dir Directory for output files. Defaults to
current working directory. [default '.']
--log-file The name of the log file. Generally
defaults to the program name in the out-dir
folder. [default '']
Engine Options (Not used on command line)
--command-line The command line executed. [default '']
--exec-guid The GUID for the process. [default '']
--program-name The name of the program [default '']
--program-company The company providing the program [default
'']
--program-version The version of the program [default '']
--program-cvs-id The CVS version of the program [default '']
--version-to-report The version to report in the output files.
[default '']
--free-mem-at-start How much physical memory was available when
the engine run started. [default '0']
--meta-data-info Meta data in key=value pair that will be
output in headers. [default '']
Input Options
--cn-reference-input The CN Reference input to the process.
[default '']
--config-file The configuration file name as passed from
GTC or the Cyto Browser. [default '']
--cychp-files Text file specifying cychp files to
process, one per line with the first line
being 'cychp_files'. [default '']
Output Options
--cn-reference-output Output CN reference file name. [default '']
Analysis Options
-a, --analysis String representing analysis pathway
desired. [default
'additional-waves-reference-method']
Misc Options
--explain Explain a particular operation (i.e.
--explain
additional-waves-reference-method).
[default '']
Advanced Options
--xChromosome X Chromosome [default '24']
--yChromosome Y Chromosome [default '25']
Engine Options (Not used on command line)
--cychps CYCHP files to process (cannot be used with
the cychp-files option). [default '']
--time-start The time the engine run was started
[default '']
--time-end The time the engine run ended [default '']
--time-run-minutes The run time in minutes. [default '']
--analysis-guid The GUID for the analysis run. [default '']
Data transformations:
additional-waves-reference-methodCopyNumber AdditionalWaves
additional-waves-reference-method: CopyNumber AdditionalWaves Parameters: 'trim' Log2Ratio Trim value. [default '2.0'] 'percentile' High Percentile value. [default '0.75'] 'additional-wave-count' Number of waves to add to the reference. [default '1'] 'demean' Demean the input to the SVD. [default 'false'] 'cn-qc-cutoff' If the CN QC values if over this cutoff then the sample fails QC. [default '0.27'] 'snp-qc-cutoff' If the SNP QC values if below this cutoff then the sample fails QC. [default '1.1'] 'waviness-seg-count-cutoff' The waviness seg count cutoff. [default '100'] 'use-high-waviness-seg-count' Use only those cychp files that have a waviness-seg-count > the cutoff if true, else use only those cychp files <= the cutoff. [default 'true'] 'force' Force the job to run even if there is a mismatch between the cychp files and the input CN reference. [default 'false'] 'keep-temp-data' If true, then do not delete the temporary data files used by the module. [default 'false']
Q. Some question? For example:
example
A. The answer.
1.7.1