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.
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
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 $
A. See the FAQ item on probe IDs for more info.
1.5.3