MANUAL: apt-copynumber-reference (apt-1.10.1)

Contents

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

Introduction

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.

Quick Start

The basic requirements for a run of apt-copynumber-reference 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-reference \
    --set-analysis-name Test \
    --hdf5-output true \
    --text-output false \	
    --log2-input false \
    --netaffx-snp-annotation-file lib_directory_name/GenomeWideSNP_6.na25.annot.csv \
    --netaffx-cn-annotation-file lib_directory_name/GenomeWideSNP_6.cn.na25.annot.csv \
    --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-reference - A program to compute copy number 
results from DNA analysis arrays.

usage:
	apt-copynumber-reference.exe \
       --genotype-report-file adapter-type-norm.quant-norm.pm-only.brlmm-p.report.txt \
       --hdf5-output true --text-output false \
       --reference-file CNReference.a5 \
       --log2-input false \
       --netaffx-snp-annotation-file snp_annot_2.csv \
       --netaffx-cn-annotation-file cn_annot_2.csv \
       -x adapter-type-norm.quant-norm.pm-only.brlmm-p.plier.summary.txt \
       --genotype-calls-file adapter-type-norm.quant-norm.pm-only.brlmm-p.calls.txt \
       --genotype-confidences-file adapter-type-norm.quant-norm.pm-only.brlmm-p.confidences.txt \
       -o apt-copynumber-reference_5_cels

options:
 Basic Info and Control Options
   -h, --help                           This message. [default 'false'] 
     --explain Explain a particular operation (i.e.
                          --explain brlmm or --explain brlmm-p).
                          [default ''] 
   -v, --verbose How verbose to be with status messages 0 -
                          quiet, 1 - usual messages, 2 - more
                          messages. [default '1'] 
     --version Output program version and quit. [default
                          'false'] 
   -o, --out-dir Directory to write result files into. Any
                          previous results in directory will be
                          overwritten. [default '.'] 
 Execution Control Options
     --mem-usage How many MB of memory to use for this run.
                          [default '0'] 
     --set-analysis-name Analysis name to use as prefix for output
                          files. [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 ''] 
     --reference-text-output Output the reference-file in acii text
                          format. [default 'false'] 
     --med-polish Use median polish summarization method
                          instead of plier. [default 'false'] 
     --log2-input Input Allele Summaries are in log2. 
                          [default 'false'] 
     --probeset-ids Tab delimited file with column 
                          'probeset_id' specifying probesets to
                          summarize. [default ''] 
     --netaffx-snp-annotation-file NetAffx SNP Annotation file. [default ''] 
     --netaffx-cn-annotation-file NetAffx CN Annotation file. [default ''] 
     --xChromosome X Chromosome [default '24'] 
     --yChromosome Y Chromosome [default '25'] 

version: apt-1.10.1 $Id: apt-copynumber-reference.cpp,v 1.27 2008/10/11 05:59:56 wshort Exp $

Frequently Asked Questions

Q. Some question? For example:

	example

A. The answer.

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