MANUAL: apt-copynumber-log2ratio (apt-1.12.0)

Contents

• Introduction.
• Quick Start
• FAQ - Frequently Asked Questions.

Introduction

apt-copynumber-log2ratio 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-log2ratio implements the portion of the workflow that generates log2ratio and allelic difference values for each probe set.

Most users will probably want to use apt-copynumber-workflow which provides a complete copynumber analysis from CEL files to CNCHP files.

Quick Start

The basic requirements for a run of apt-copynumber-log2ratio are:

• Output from a run of apt-probeset-genotype including hdf5 formatted signal estimates, genotype calls, and genotype confidences; and an ascii text formatted report file. In addition, the global hdf5 file output from apt-probeset-genotype containing the target-sketch, feature-effects, and snp-posteriors.

• Annotation files (GenomeWide SNP 6.0) consisting of the SNP IDs annotated by chromosome, position, and other covariates needed in normalization; and Copy Number IDs annotated similarly. These files can be downloaded from the Affymetrix array support page at http://www.affymetrix.com/support/technical/byproduct.affx?cat=dnaarrays

• A directory where results will be stored. For this example it is called 'output_directory_name'

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-log2ratio \
    --set-analysis-name Test \
    --log2-input false \
    --hdf5-output true \
    --text-output false \
    --cnchp-output false \
    --call-copynumber 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

Options:

	./apt-copynumber-log2ratio \
		 -v 3 \
		 --log2-input false \
		 --log2ratio-hdf5-output true \
		 --log2ratio-text-output true \
		 --text-output false \
		 --cnchp-output false \
		 --cychp-output false \
		 --call-copynumber-engine 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 \
		 --reference-file test-generated/GenomeWideSNP_6/component_6_cels/CNReference.a5.ref \
		 --genotype-report-file test-generated/GenomeWideSNP_6/component_6_cels/CN5.report.txt \
		 --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 \
		 --geno-qc-file test-generated/GenomeWideSNP_6/component_6_cels/apt-geno-qc.txt

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'] 
     --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'] 
 Input Options
     --probeset-ids Tab delimited file with column 
                          'probeset_id' specifying probesets to
                          summarize. [default ''] 
     --annotation-file NetAffx Annotation file. [default ''] 
     --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
     --call-copynumber-engine Call the copy number engine to output CNCHP
                          files. [default 'true'] 
     --log2ratio-hdf5-output Write intermediate output in HDF5 format.
                          [default 'false'] 
     --log2ratio-text-output Write intermediate output in ASCII Text
                          format. [default 'false'] 
 Advanced Options
     --xChromosome X Chromosome [default '24'] 
     --yChromosome Y Chromosome [default '25'] 
     --gc-correction-bin-count The number of bins to use for GC content.
                          [default '25'] 
 Execution Control Options
     --mem-usage How many MB of memory to use for this run.
                          [default '0'] 
 Additional CNLog2RatioEngine Options
   -a, --analysis String representing analysis pathway
                          desired. [default ''] 
     --delete-files Delete extra output files after the run has
                          completed. [default 'false'] 
     --log2-input Input Allele Summaries are in log2. 
                          [default 'false'] 
     --gc-content-override-file Input file used to override the GC content
                          read from the annotation file (Two columns
                          with header line, ProbeSetName/GCContent).
                          [default ''] 
 Additional CNAnalysisEngine Options
     --geno-qc-file The file output from GenoQC. [default ''] 
     --cyto2 Processing CYTO2 chip. [default 'false'] 
     --array-name Array name or type to use. [default ''] 
     --set-analysis-name Analysis name to use as prefix for output
                          files. [default ''] 
     --text-output Output data in ASCII text format in 
                          addition to calvin format. [default 
                          'false'] 
     --cnchp-output Report CNCHP files [default 'true'] 
     --cychp-output Report CYCHP files [default 'false'] 
     --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 ''] 

Frequently Asked Questions

Q. Some question? For example:

	example

A. The answer.