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

Contents

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

Introduction

apt-copynumber-analysis 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-analysis implements the portion of the workflow that generates cn-state, loh, and gaussian smooth 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-analysis are:

• Output from a run of apt-copynumber-log2ratio consisting of an hdf5 formatted intermediate file.

• 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-analysis \
    --array-name GenomeWideSNP_6 \
    --text-output true \
    --set-analysis-name Test \
    --log2ratio-file input_directory/Test.NA06985_GW6_C.cel.a5 \
    --out-dir output_directory_name

Options:

	apt-copynumber-analysis.exe \
     --text-output true \
     --set-analysis-name apt-copynumber-analysis \
     --log2ratio-file Test.NA06985_GW6_C.cel.a5 \
     -o apt-copynumber-analysis

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 '.'] 
     --mem-usage How many MB of memory to use for this run.
                          [default '0'] 
 Execution Control Options
   -a, --analysis String representing analysis pathway
                          desired. [default ''] 
     --log2ratio-file Log2Ratio file. [default ''] 
     --xChromosome X Chromosome. [default '24'] 
     --yChromosome Y Chromosome. [default '25'] 
     --geno-qc-file The file output from GenoQC. [default ''] 
     --cyto2 Processing CYTO2 chip. [default 'false'] 
     --CN2Gender-MAPD-threshold The MAPD cutoff threshold for CN2 gender
                          calling. [default '0.5'] 
     --CN2Gender-male-ChrX-lower-threshold The male CN call lower threshold for
                          chromosome X CN2 gender calling. [default
                          '0.8'] 
     --CN2Gender-male-ChrX-upper-threshold The male CN call upper threshold for
                          chromosome X CN2 gender calling. [default
                          '1.3'] 
     --CN2Gender-male-ChrY-lower-threshold The male CN call lower threshold for
                          chromosome Y CN2 gender calling. [default
                          '0.8'] 
     --CN2Gender-male-ChrY-upper-threshold The male CN call upper threshold for
                          chromosome Y CN2 gender calling. [default
                          '1.2'] 
     --CN2Gender-female-ChrX-lower-threshold The female CN call lower threshold for
                          chromosome X CN2 gender calling. [default
                          '1.9'] 
     --CN2Gender-female-ChrX-upper-threshold The female CN call upper threshold for
                          chromosome X CN2 gender calling. [default
                          '2.1'] 
     --CN2Gender-female-ChrY-lower-threshold The female CN call lower threshold for
                          chromosome Y CN2 gender calling. [default
                          '0'] 
     --CN2Gender-female-ChrY-upper-threshold The female CN call upper threshold for
                          chromosome Y CN2 gender calling. [default
                          '0.4'] 
     --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'] 

Data transformations:
   cn-state          CopyNumber CNState 
   gaussian-smooth   CopyNumber GaussianSmooth 
   loh               CopyNumber LOH 
   cn-neutral-loh    Copynumber CNNeutralLOH 
   normal-diploid    Copynumber NormalDiploid 
   mosaicism         Copynumber Mosaicism 
   no-call           Copynumber NoCall 

version: apt-1.10.1 $Id: apt-copynumber-analysis.cpp,v 1.34 2008/10/24 06:08:52 awilli Exp $

Frequently Asked Questions

Q. Some question? For example:

	example

A. The answer.

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