MANUAL: apt-copynumber-log2ratio (apt-1.10.1)

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 \
    --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-log2ratio.exe \
       --set-analysis-name Test \
       --log2-input false --hdf5-output true \
       --text-output true --cnchp-output true \
       --call-copynumber true \
       --netaffx-snp-annotation-file snp_annot_2.csv \
       --netaffx-cn-annotation-file cn_annot_2.csv \
       --reference-file CNReference.a5 \
       --genotype-report-file adapter-type-norm.quant-norm.pm-only.brlmm-p.report.txt \
       -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-log2ratio_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
     --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 ''] 
     --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 ''] 
     --xChromosome X Chromosome [default '24'] 
     --yChromosome Y Chromosome [default '25'] 
     --reference-file Copy Number Reference file. [default ''] 
     --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'] 
     --mem-usage How many MB of memory to use for this run.
                          [default '0'] 
     --med-polish Use median polish summarization method
                          instead of plier. [default 'false'] 
   -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'] 
     --median-autosome-median-normalization Perform the median autosomal median
                          normalization step. [default 'true'] 
     --yTarget Y Target [default '0.6748'] 
     --allelic-difference-outlier-trim Allele Diff Outlier Trim [default '3'] 
     --gc-correction Apply the GC correction to the Log2Ratios
                          and Allelic Differences. [default 'true'] 
     --gc-content-override-file Input file used to override the GC content
                          read from the annotation files (Two columns
                          with header line, ProbeSetName/GCContent).
                          [default ''] 
     --gc-correction-bin-count The number of bins to use when applying the
                          gc-correction. [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-log2ratio.cpp,v 1.38 2008/10/24 06:08:52 awilli Exp $

Frequently Asked Questions

Q. Some question? For example:

	example

A. The answer.

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