MANUAL: apt-geno-qc (apt-1.10.1)

Contents

• Introduction.
• Quick Start - getting up and running.
• The Report File - explanation of contents.
• Program Options - command line options.

Introduction

apt-geno-qc is a program for making statistical assessements of experimental qualities from Affymetrix SNP microarrays using the model based algorithm DM.

As DM is a single sample model based algorithm it processes one CEL file a time in a multiple CEL file batch. Since DM requires MM existence apt-geno-qc only operates on SNPs tiled with mismatches, therefore, apt-geno-qc works on all SNPs on Mapping500K, but only works on a small subset of SNPs on SNP5 and SNP6 tiled for QC purposes (FQC SNPs).

The current option to output DM calls (see --dm-out) is experimental. This feature may go away or it may be moved into a separate program to generate DM calls.

Quick Start

We illustrate the most basic way to run apt-geno-qc with an example. This example runs an analysis under the default parameter settings to generate a report file containing QC statistics for each CEL file with each specified method (or same method with different parameters). The requirements are:

• A collection of CEL files to process (one or many). For this example the CEL files specified by a CEL file list file with full pathes to each of the CEL files.
• The CDF file corresponding to the array type of the CELs. For this example the CDF file is called 'Mapping250K_Sty.cdf'. It can be downloaded from http://www.affymetrix.com/support/technical/libraryfilesmain.affx
• A file name with full path specified which you want the results to be writen
• A apt-geno-qc configuration file with methods and associated parameters specified

A 500K example:

apt-geno-qc \
  --cdf-file Mapping250K_Sty.cdf \
  --qca-file Mapping250K_Sty.qca \
  --qcc-file Mapping250K_Sty.qcc \
  --cel-files cel_file_list.txt \
  --out-file results.txt

A SNP5 example:

apt-geno-qc \
  --cdf-file GenomeWideSNP_5.cdf \
  --qca-file GenomeWideSNP_5.qca \
  --qcc-file GenomeWideSNP_5.qcc \
  --cel-files cel_file_list.txt \
  --out-file results.txt

A SNP6 example:

apt-geno-qc \
  --cdf-file GenomeWideSNP_6.cdf \
  --qca-file GenomeWideSNP_6.r2.qca \
  --qcc-file GenomeWideSNP_6.r2.qcc \
  --chrX-probes GenomeWideSNP_6.chrXprobes \
  --chrY-probes GenomeWideSNP_6.chrYprobes \
  --cel-files cel_file_list.txt \
  --out-file results.txt

The Report File

apt-geno-qc creates a report file with file name specified by -o or --out-file option. The report file contains QC stats to measure the experimental quality for each CEL file. The format of the file is tab-delimited text with a header followed by a column header, then a line for each CEL file analyzed and a column for each method specified in the configuration file. The header contains information of which CDF file is used and what kind of methods are used for generating QC stats, and parameters associated with each method. The column entries are:

1. The CEL file name.
2. The stats for each method, variable number of columns equal to number of methods in the configuration file

Options:

apt-geno-qc - a single-chip-based genotyping chip quality control tool,
it reports one or more metrics for each chip analyzed.  The metrics
computed are determined by one of the supplied input files (the qca file).

usage:
  apt-geno-qc.exe --cdf-file my_chip.cdf --qcc-file my_chip.qcc \
    --qca-file my_chip.qca --out-file my_output.txt \
    --cel-files my_cel_files.txt

  apt-geno-qc.exe -c my_chip.cdf -q my_chip.qcc -a my_chip.qca \
    -o my_output.txt --cel-files my_cel_files.txt


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'] 
 Input Options
     --xml-file Input parameters in XML format (Will
                          override command line settings). [default
                          ''] 
     --cdf-file File defining probe sets. [default ''] 
     --spf-file SPF File defining probe sets. [default ''] 
   -q, --qcc-file File defining QC probesets. [default ''] 
   -a, --qca-file File defining QC analysis methods. [default
                          ''] 
     --cel-files Text file specifying cel files to process,
                          one per line with the first line being
                          'cel_files'. [default ''] 
     --chrX-probes File containing probe_id (1-based) of 
                          probes on chrX. Used for copy number probe
                          chrX/Y ratio gender calling. [Experimental]
                          [default ''] 
     --chrY-probes File containing probe_id (1-based) of 
                          probes on chrY. Used for copy number probe
                          chrX/Y ratio gender calling. [Experimental]
                          [default ''] 
     --probe-class-file File containing probe_id (1-based) of 
                          probes and a 'class' designation. Used to
                          compute mean probe intensity by class for
                          report file. [default ''] 
 Output Options
   -o, --out-file Name to use for the output file. [default
                          ''] 
     --dm-out Folder to use for DM output. Enables DM
                          output. One per CEL file. [experimental]
                          [default ''] 
 Analysis Options
     --dm-het-mult DM Het Mult to use for DM output. [default
                          '1.25'] [default '1.25'] 
     --dm-thresh DM threshold to use for making no calls.
                          [default '0.33'] [default '0.33'] 
   -f, --force Don't check the chip types, just assume 
                          they match. [default 'false'] [default
                          'false'] 
 Execution Control Options

Standard Methods:

version: apt-1.10.1 $Id: apt-geno-qc.cpp,v 1.42 2008/10/01 22:45:39 harley Exp $

Frequently Asked Questions

Q. What is a probe_id?

A. See the FAQ item on probe IDs for more info.

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