apt-copynumber-reference is a component of the CN5 suite of applications for finding de novo copy number changes and Loss of Heterozygosity (LOH) on a per sample basis with respect to a reference set of samples. The copy number algorithm it implements assumes that the reference set comprises a mix of normal human males (with XY chromosomes) and normal human females (with XX chromosomes). The algorithms assume that in this reference for each autosomal marker (SNP or Copy Number probe) the predominant Copy Number is 2, and for the sex chromosomes the copy number is determined by the gender.
apt-copynumber-reference implements the portion of the workflow that loads median probeset values into the CN5 reference file.
Most users will probably want to use apt-copynumber-workflow which provides a complete copynumber analysis from CEL files to CNCHP files.
The basic requirements for a run of apt-copynumber-reference are:
On unix systems a basic command using the default parameters to do a batch run on GenomeWide SNP 6.0 data would look like:
apt-copynumber-reference \
--set-analysis-name Test \
--hdf5-output true \
--text-output false \
--log2-input false \
--annotation-file lib_directory_name/GenomeWideSNP_6.na28.annot.db \
--reference-file input_directory_name/CNReference.a5.ref \
--x input_directory_name/Test.plier.summary.a5 \
--genotype-calls-file input_directory_name/Test.calls.a5 \
--genotype-confidences-file input_directory_name/Test.confidences.a5 \
--genotype-report-file input_directory_name/Test.report.txt \
--out-dir output_directory_name
apt-copynumber-reference - A program to compute copy number
results from DNA analysis arrays.
usage:
./apt-copynumber-reference \
-v 3 \
--genotype-report-file test-generated/GenomeWideSNP_6/component_6_cels/CN5.report.txt \
--reference-text-output false \
--reference-file test-generated/GenomeWideSNP_6/component_6_cels/CNReference.a5.ref \
--log2-input false \
--netaffx-snp-annotation-file ../../../regression-data/data/lib/GenomeWideSNP_6/GenomeWideSNP_6.na26.1.annot.csv \
--netaffx-cn-annotation-file ../../../regression-data/data/lib/GenomeWideSNP_6/GenomeWideSNP_6.cn.na26.1.annot.csv \
--expr-summary-file test-generated/GenomeWideSNP_6/component_6_cels/CN5.plier.summary.a5 \
--genotype-calls-file test-generated/GenomeWideSNP_6/component_6_cels/CN5.calls.a5 \
--genotype-confidences-file test-generated/GenomeWideSNP_6/component_6_cels/CN5.confidences.a5 \
--out-dir test-generated/GenomeWideSNP_6/component_6_cels
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
--expr-summary-file Expression Summary Table file. [default '']
--genotype-calls-file Genotype Calls Table file. [default '']
--genotype-confidences-file Genotype Confidences Table file. [default
'']
--genotype-report-file Genotype Report Table file. [default '']
--reference-file Copy Number Reference file. [default '']
Output Options
--reference-text-output Output the reference-file in acii text
format. [default 'false']
Analysis Options
--log2-input Input Allele Summaries are in log2.
[default 'false']
--adapter-type-normalization Adapter Type Normalization option. true =
perform adapter type normalization.
[default 'true']
Advanced Options
--set-analysis-name Analysis name to use as prefix for output
files. [default '']
Execution Control Options
--mem-usage How many MB of memory to use for this run.
[default '0']
Additional CNReferenceEngine Options
--probeset-ids Tab delimited file with column
'probeset_id' specifying probesets to
summarize. [default '']
--annotation-file NetAffx Annotation file. [default '']
--xChromosome X Chromosome [default '24']
--yChromosome Y Chromosome [default '25']
--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 '']
Q. Some question? For example:
example
A. The answer.
1.7.1