apt-summary-genotype - Utility program to feed an allele summary file directly into
a genotype calling Quant method. Currenlty on brlmm-p is supported.
usage:
./apt-summary-genotype -p CM=1.bins=100.K=2.SB=0.003.MS=0.05 \
-o results \
-s brlmm-p.plier.summary.txt \
--read-models-brlmmp GenomeWideSNP_5.models \
--chrX-snps GenomeWideSNP_5.chrx \
--read-genders genders.txt
options:
Common Options (not used by all programs)
-h, --help Display program options and extra
documentation about possible analyses. See
-explain for information about a specific
operation. [default 'false']
-v, --verbose How verbose to be with status messages 0 -
quiet, 1 - usual messages, 2 - more
messages. [default '1']
--console-off Turn off the default messages to the
console but not logging or sockets.
[default 'false']
--use-socket Host and port to print messages over in
localhost:port format [default '']
--version Display version information. [default
'false']
-f, --force Disable various checks including chip
types. Consider using --chip-type option
rather than --force. [default 'false']
--throw-exception Throw an exception rather than calling
exit() on error. Useful for debugging. This
option is intended for command line use
only. If you are wrapping an Engine and
want exceptions thrown, then you should
call Err::setThrowStatus(true) to ensure
that all Err::errAbort() calls result in an
exception. [default 'false']
--analysis-files-path Search path for analysis library files.
Will override AFFX_ANALYSIS_FILES_PATH
environment variable. [default '']
--xml-file Input parameters in XML format (Will
override command line settings). [default
'']
--temp-dir Directory for temporary files when working
off disk. Using network mounted drives is
not advised. When not set, the output
folder will be used. The defaut is
typically the output directory or the
current working directory. [default '']
-o, --out-dir Directory for output files. Defaults to
current working directory. [default '.']
--log-file The name of the log file. Generally
defaults to the program name in the out-dir
folder. [default '']
Engine Options (Not used on command line)
--command-line The command line executed. [default '']
--exec-guid The GUID for the process. [default '']
--program-name The name of the program [default '']
--program-company The company providing the program [default
'']
--program-version The version of the program [default '']
--program-cvs-id The CVS version of the program [default '']
--version-to-report The version to report in the output files.
[default '']
--free-mem-at-start How much physical memory was available when
the engine run started. [default '0']
--meta-data-info Meta data in key=value pair that will be
output in headers. [default '']
-p, --algo-params A string specifying algo parameters. See
--explain option for acceptable parameters.
[default '']
--file5-summaries Interleaved Allele summaries file in file5
format with summaries in /summaries group.
[default '']
-s, --summaries Interleaved Allele summaries file. [default
'']
--summaries-a Allele summarie file for A allele. [default
'']
--summaries-b Allele summarie file for B allele. [default
'']
--file5-output Should output be formatted in file5 (hdf5)
output. [default 'false']
--chrX-snps File containing snps on chrX
(non-pseudoautosomal region). [default '']
--special-snps File containing all snps of unusual copy
(chrX,mito,Y) [default '']
--special-sample-snps File containing all sample-specific snps of
unusual copy [default '']
--write-models Should we write snp specific models out for
analysis? [experimental] [default 'false']
--read-models-brlmmp File to read precomputed BRLMM-P snp
specific models from. [default '']
--read-genders Explicitly read genders from a file.
[default '']
--genotypes File to read seed genotypes from. [default
'']
--select-probes Should we evaluate model fit for clusters
by probe-set/probe[experimental] [default
'false']
--set-analysis-name Explicitly set the analysis name. This
affects output file names (ie prefix) and
various meta info. [default '']
--time-start The time the engine run was started
[default '']
--time-end The time the engine run ended [default '']
--time-run-minutes The run time in minutes. [default '']
--analysis-guid The GUID for the analysis run. [default '']
The genders file is a TSV file (tab separated) with a header line followed by data lines. The header must contain a "cel_files" column and a "gender" column. The values in the "cel_files" column must match up with the headers in the allele summary file. Here is an example:
apt-summary-genotype - Utility program to feed an allele summary file directly into
a genotype calling Quant method. Currenlty on brlmm-p is supported.
usage:
./apt-summary-genotype -p CM=1.bins=100.K=2.SB=0.003.MS=0.05 \
-o results \
-s brlmm-p.plier.summary.txt \
--read-models-brlmmp GenomeWideSNP_5.models \
--chrX-snps GenomeWideSNP_5.chrx \
--read-genders genders.txt
options:
Common Options (not used by all programs)
-h, --help Display program options and extra
documentation about possible analyses. See
-explain for information about a specific
operation. [default 'false']
-v, --verbose How verbose to be with status messages 0 -
quiet, 1 - usual messages, 2 - more
messages. [default '1']
--console-off Turn off the default messages to the
console but not logging or sockets.
[default 'false']
--use-socket Host and port to print messages over in
localhost:port format [default '']
--version Display version information. [default
'false']
-f, --force Disable various checks including chip
types. Consider using --chip-type option
rather than --force. [default 'false']
--throw-exception Throw an exception rather than calling
exit() on error. Useful for debugging. This
option is intended for command line use
only. If you are wrapping an Engine and
want exceptions thrown, then you should
call Err::setThrowStatus(true) to ensure
that all Err::errAbort() calls result in an
exception. [default 'false']
--analysis-files-path Search path for analysis library files.
Will override AFFX_ANALYSIS_FILES_PATH
environment variable. [default '']
--xml-file Input parameters in XML format (Will
override command line settings). [default
'']
--temp-dir Directory for temporary files when working
off disk. Using network mounted drives is
not advised. When not set, the output
folder will be used. The defaut is
typically the output directory or the
current working directory. [default '']
-o, --out-dir Directory for output files. Defaults to
current working directory. [default '.']
--log-file The name of the log file. Generally
defaults to the program name in the out-dir
folder. [default '']
Engine Options (Not used on command line)
--command-line The command line executed. [default '']
--exec-guid The GUID for the process. [default '']
--program-name The name of the program [default '']
--program-company The company providing the program [default
'']
--program-version The version of the program [default '']
--program-cvs-id The CVS version of the program [default '']
--version-to-report The version to report in the output files.
[default '']
--free-mem-at-start How much physical memory was available when
the engine run started. [default '0']
--meta-data-info Meta data in key=value pair that will be
output in headers. [default '']
-p, --algo-params A string specifying algo parameters. See
--explain option for acceptable parameters.
[default '']
--file5-summaries Interleaved Allele summaries file in file5
format with summaries in /summaries group.
[default '']
-s, --summaries Interleaved Allele summaries file. [default
'']
--summaries-a Allele summarie file for A allele. [default
'']
--summaries-b Allele summarie file for B allele. [default
'']
--file5-output Should output be formatted in file5 (hdf5)
output. [default 'false']
--chrX-snps File containing snps on chrX
(non-pseudoautosomal region). [default '']
--special-snps File containing all snps of unusual copy
(chrX,mito,Y) [default '']
--special-sample-snps File containing all sample-specific snps of
unusual copy [default '']
--write-models Should we write snp specific models out for
analysis? [experimental] [default 'false']
--read-models-brlmmp File to read precomputed BRLMM-P snp
specific models from. [default '']
--read-genders Explicitly read genders from a file.
[default '']
--genotypes File to read seed genotypes from. [default
'']
--select-probes Should we evaluate model fit for clusters
by probe-set/probe[experimental] [default
'false']
--set-analysis-name Explicitly set the analysis name. This
affects output file names (ie prefix) and
various meta info. [default '']
--time-start The time the engine run was started
[default '']
--time-end The time the engine run ended [default '']
--time-run-minutes The run time in minutes. [default '']
--analysis-guid The GUID for the analysis run. [default '']
The allele summaries file is a TSV file (tab separated) with a header line followed by data lines. The header must contain a "probeset_id" column in the first column followed by a column for each sample. There are two rows for each SNP. The first row is the allele summaries (estimates) for the A allele. The second row is the summaries for the B allele. This is further indicated by the suffix "-A" and "-B" to the probeset ID in the first column. Here is an example:
apt-summary-genotype - Utility program to feed an allele summary file directly into
a genotype calling Quant method. Currenlty on brlmm-p is supported.
usage:
./apt-summary-genotype -p CM=1.bins=100.K=2.SB=0.003.MS=0.05 \
-o results \
-s brlmm-p.plier.summary.txt \
--read-models-brlmmp GenomeWideSNP_5.models \
--chrX-snps GenomeWideSNP_5.chrx \
--read-genders genders.txt
options:
Common Options (not used by all programs)
-h, --help Display program options and extra
documentation about possible analyses. See
-explain for information about a specific
operation. [default 'false']
-v, --verbose How verbose to be with status messages 0 -
quiet, 1 - usual messages, 2 - more
messages. [default '1']
--console-off Turn off the default messages to the
console but not logging or sockets.
[default 'false']
--use-socket Host and port to print messages over in
localhost:port format [default '']
--version Display version information. [default
'false']
-f, --force Disable various checks including chip
types. Consider using --chip-type option
rather than --force. [default 'false']
--throw-exception Throw an exception rather than calling
exit() on error. Useful for debugging. This
option is intended for command line use
only. If you are wrapping an Engine and
want exceptions thrown, then you should
call Err::setThrowStatus(true) to ensure
that all Err::errAbort() calls result in an
exception. [default 'false']
--analysis-files-path Search path for analysis library files.
Will override AFFX_ANALYSIS_FILES_PATH
environment variable. [default '']
--xml-file Input parameters in XML format (Will
override command line settings). [default
'']
--temp-dir Directory for temporary files when working
off disk. Using network mounted drives is
not advised. When not set, the output
folder will be used. The defaut is
typically the output directory or the
current working directory. [default '']
-o, --out-dir Directory for output files. Defaults to
current working directory. [default '.']
--log-file The name of the log file. Generally
defaults to the program name in the out-dir
folder. [default '']
Engine Options (Not used on command line)
--command-line The command line executed. [default '']
--exec-guid The GUID for the process. [default '']
--program-name The name of the program [default '']
--program-company The company providing the program [default
'']
--program-version The version of the program [default '']
--program-cvs-id The CVS version of the program [default '']
--version-to-report The version to report in the output files.
[default '']
--free-mem-at-start How much physical memory was available when
the engine run started. [default '0']
--meta-data-info Meta data in key=value pair that will be
output in headers. [default '']
-p, --algo-params A string specifying algo parameters. See
--explain option for acceptable parameters.
[default '']
--file5-summaries Interleaved Allele summaries file in file5
format with summaries in /summaries group.
[default '']
-s, --summaries Interleaved Allele summaries file. [default
'']
--summaries-a Allele summarie file for A allele. [default
'']
--summaries-b Allele summarie file for B allele. [default
'']
--file5-output Should output be formatted in file5 (hdf5)
output. [default 'false']
--chrX-snps File containing snps on chrX
(non-pseudoautosomal region). [default '']
--special-snps File containing all snps of unusual copy
(chrX,mito,Y) [default '']
--special-sample-snps File containing all sample-specific snps of
unusual copy [default '']
--write-models Should we write snp specific models out for
analysis? [experimental] [default 'false']
--read-models-brlmmp File to read precomputed BRLMM-P snp
specific models from. [default '']
--read-genders Explicitly read genders from a file.
[default '']
--genotypes File to read seed genotypes from. [default
'']
--select-probes Should we evaluate model fit for clusters
by probe-set/probe[experimental] [default
'false']
--set-analysis-name Explicitly set the analysis name. This
affects output file names (ie prefix) and
various meta info. [default '']
--time-start The time the engine run was started
[default '']
--time-end The time the engine run ended [default '']
--time-run-minutes The run time in minutes. [default '']
--analysis-guid The GUID for the analysis run. [default '']
Q. What is the minimum input?
A. You can run the program with only an allele summary file. In this senario all genders are assumed unknown (which BRLMM-P treats as female) and all SNPs are considered diploid.
1.7.1