The Analysis Power Tools (APT) is a collection of command line programs
for analyzing and working with Affymetrix microarray data. These programs are
generally focused on CEL file level analysis. APT also refers to the underlying
C++ source code. Binaries and source code are available from the main APT
website, http://www.affymetrix.com/support/developer/powertools/index.affx.
Power User Manuals
Power user manuals are available for specific command line applications:
- Main Applications:
- apt-genotype-axiom: A program for performing recommended genotype calling analysis on Axiom arrays.
- apt-summary-genotype-axiom: A program that enables genotyping using a summary.a5 or .txt file as input, rather than CEL files.
- apt-geno-qc: A program for doing
single chip QC of WGSA genotyping arrays.
- apt-probeset-genotype: A
program for analyzing mapping arrays. Supports BRLMM-P, Birdseed, and
BRLMM methods for genotype calling.
- apt-copynumber-axiom-cnvmix:
A program that reports copy number in predefined regions with dynamic copy number state thresholds. Also reports loss of heterozygosity states.
- apt-copynumber-axiom-hmm:
A program that reports copy number and loss of heterozygosity states using a hidden Markov model.
- apt-copynumber-axiom-ref:
A program that generates a copy number reference model library file used by other copy number engines.
- apt-copynumber-axiom-safer:
A program that reports copy number in predefined regions with fixed copy number state thresholds. Also reports loss of heterozygosity states. Renamed from apt-copynumber-axiom-ssa.
- apt-dmet-genotype: A program to
compute genotypes and copy number variation from DMET Plus CEL files.
DMET CHP files are generated.
- apt-dmet-translation: A
program to compute star allele translation reports from DMET Plus CHP
files.
- apt-copynumber-cyto-ssa: A
program to run single-sample copynumber and LOH analysis on CytoScan
family of arrays.
- apt-copynumber-cyto-ref: A
program to generate reference model files for copynumber and LOH
analysis of CytoScan family of arrays.
- apt-copynumber-wave: A program
to add additional waves to copynumber reference file. Most users should
use default wave corrections provided by ThermoFisher.
- apt-canary: A program to compute copy
number variation calls given a known set of CNV regions.
- apt-copynumber-onco-ref: A
program to generate copynumber reference model files for OncoScan
arrays.
- apt-copynumber-onco-ssa: A
program to perform copynumber analysis on OncoScan arrays and matched
normal/tumor pairs.
- apt-copynumber-onco-som-ref:
A program to generate somatic mutation reference model files for
OncoScan arrays.
- apt-copynumber-onco-som-ssa:
A program to implement the somatic mutation analysis pipeline for
OncoScan arrays
- ps-metrics: A program to generate
various QC metrics for SNPs for Axiom arrays.
- ps-classification: A program
which reads a metrics table generated by ps-metrics and classifies SNPs
based on a number of customizable criteria.
- otv-caller: A program for identifying
off-target variants.
- apt-genotype-eureka: A program
for performing recommended genotype calling analysis on Eureka binning
files.
- nibls: A program for converting sequence
data from the Eureka platform into binning files to be used in
genotyping or visualization.
- apt-probeset-summarize: A
program for analyzing expression arrays including 3' IVT and exon
arrays. Supports background correction (MAS5,RMA), normalization
(linear scaling, quantile, sketch), and summarization (PLIER, RMA,
MAS5) methods.
- Utility Programs:
- ps-call-adjust:Rewrites any genotype call to "No Call" where the call's confidence score fails a user-specified threshold, and outputs a calls file with the adjusted calls. To adjust only a given set of probesets, use a probeset list file with probeset_id as the first line. More details describing the use of `ps-call-adjust`.
- ps-extract:extracts data from calls, confidences, summary, references, posteriors (biallelic and multiallelic), and priors (biallelic and multiallelic) files for a supplied set of probesets and/or samples. Every input file has a matching output file.
- ps-bac:Tests for batch effects when samples were genotyped in batches.
- apt2-summary-file-util:Application that converts summary.a5 to .txt file format and summary.txt to summary.a5 format.
- apt-sample-util:
A program that splits samples by plate barcode from report, summary, confidence and calls files.
- apt-cel-transformer: A program
for applying arbitrary chipstream methods (ie quantile normalization,
RMA background correction) to a set of cel files, resulting in a new
set of cel files.
- apt-cel-extract: A program for
extracting feature level intensities from CEL files.
- apt-cel-convert: A program for
converting CEL files to different formats.
- apt-chp-to-txt: A program to dump
AGCC and XDA chp files as text.
- apt-file5-util: A program to
convert between a5 and text formats.
- apt-engine-wrapper: A program
to directly call analysis engines. The main use is to run it with the
help option in order to find out what options various sub-engines will
except.
- apt-annotation-converter:
A program to create custom SQLite format annotation files from csv
files.
- apt2-dset-util: A program for
converting between the file formats supported by the APT2 framework,
including OSCHP and text files (Supports up to 500 samples).
- apt-param-convert: A program for
converting XML parameter files used in legacy applications to those
used in newer APT2 applications (e.g. from apt-probeset-genotype to
apt-genotype-axiom).
- apt-package-util: A program for
creating batch folder used by Axiom Analysis Suite from output produced by APT or GTC.
- apt-format-result: A program for
creating VCF or PLINK file formats from Axiom Analysis Suite output files.
- apt-copynumber-format-igv: A program for exporting probe and segment
level data into a format compatible with the Integrative Genome Viewer
(IGV).
- apt-suitcase-extract: A
program for converting .suitcase files generated by Axiom Analysis
Suite version 1 to folder format required by version 1.1.
- Legacy Programs (likely to be removed in later APT releases):
- apt-midas: A program to compute MiDAS
(alternative splice detection) scores from exon array results.
- apt-summary-genotype: A
program to run BRLMM-P family of algorithms on allele summaries.
- apt-copynumber-workflow: A program to run the copy number analysis workflow on SNP6 arrays.
More Detailed Documentation
For specific details see:
- Index.html: This document
- Install.html: Notes on how to install APT
- Change.html: Specific changes associated with
each release version
- Vignette.html: List of vignettes available
for APT. Vignettes are brief and concise documents on specific topics.
- FAQ.html: List of FAQs pertaining to the whole of
APT. Program and application FAQ items are listed in program manuals and
application vignettes.
- File-Formats.html: Information about file
formats used by APT.
History and Changes
The APT code provides the back end analysis engine for Expression Console
and Genotype Console. The APT packaged evolved out of an early exon array
analysis package called ExACT. All users should review the Change Log for details on changes made to APT.
Changes to algorithm behavior and the addition of new features will be itemized
in the Change Log. The latest information and downloads for APT are available
on the APT
DevNet website.
Compute Platforms
See the Platforms page for more information.
Support
Support for APT is handled through the Affymetrix Developer Network.
Specifically, questions, problems, feature requests, and other inquiries should
be made through the Developer Network email address, devnet@affymetrix.com. To get emails
updates about APT or to view previous APT announcements see the APT
User Form.
APT is not supported through the Affymetrix call center, Field Application
Specialists, or other standard Affymetrix Technical Support channels.
NO WARRANTY
THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT
LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT,
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely
responsible for determining the appropriateness of using and distributing the
Program and assumes all risks associated with its exercise of rights under this
Agreement, including but not limited to the risks and costs of program errors,
compliance with applicable laws, damage to or loss of data, programs or
equipment, and unavailability or interruption of operations.
DISCLAIMER OF LIABILITY
NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY
OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF
THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF
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Analysis Power Tools (APT) Release 2.11.4
