apt-copynumber-cyto is a program 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-cyto implements two distinct workflows, a reference workflow that uses as a a set of CEL files that are input to outputs one or more reference files including copynumber and SNP information; and conceptually, a single-sample workflow that compares each CEL file to a pre-computed reference for analysis. For efficiency of computation the "single-sample workflow" operates on a set of input CEL files at a time, but the output for any CEL file is unaffected by any of the other CEL files.
For CytoScanHD the following library files are required to run apt-copynumber-cyto:
CytoScanHD_Array.na32.annot.db: NetAffx Annotation database file. It is a SQLite 3.x database.
CytoScanHD_Array.chrXprobes: An ASCII file that contains probe_id (1-based) of
probes on chrX. Used for copy number probe chrX/Y ratio gender calling.
CytoScanHD_Array.chrYprobes: An ASCII file that contains probe_id (1-based) of
probes on chrY as column 1 and probeset_id as column 2. Probe_id is used for
copy number probe chrX/Y ratio gender calling and probeset_id is used for
hasY gender call and Y-Gender call.
CytoScanHD_Array.r1.qca: An ASCII file that defines the parameters for the calculations of qc-call-rate
and contrast-qc-rand that are used in the geno-qc analysis.
CytoScanHD_Array.r1.qcc: An ASCII file that defines the probesets that are used by the geno-qc analysis
CytoScanHD_Array.cdf: Chip definition file (binary file).
CytoScanHD_Array.probe_tab: An ASCII file that contains probe sequence information. (Reference creation only).
CytoScanHD_Array.hg19.v3.refcovar: An hdf5 format file that contains covariate information for each probeset, where
the first column is the probeset name and subsequent column(s) are covariates in float.
(Reference creation only).
CytoScanHD_Array.snplist.txt: An ASCII file that contains SNP probeset_id that are used to compute processed SNPQC and Raw SNPQC.
The first row of the file must be "probeset_id". (Single sample mode processing only).
CytoScanHD_Array.na32.v3.REF_MODEL: Affymetrix copy number reference generated from a set of hapmaps and normal blood samples (hdf5 format file).
See 2.7M cytogenetics vignette for libraries and requirements for 2.7M analysis.
apt-copynumber-cyto can be applied to multiple chip types, including Cyto 2.7M and CytoScanHD. Since different chip types require different analysis option and steps, the default parameter values may not always be appropriate to a chip type or the particular annotation files for that chip type. We strongly recommend all parameters be explicitly specified.
On unix systems, a command to build a reference for CytoScanHD data would look like this:
NOTE: This command needs to have the comments removed to be runnable, as they break the unix shell syntax. The comments and additional spaces are to clarify the options being used. The arguments which are joined with a "."s should be joined without spaces.
apt-copynumber-cyto -v 4 \ #verbose output level in the log file ranging from 1 (least details) to 4 (most details) --cyto2 false \ #true: Cytogenetics_Array; false: CytoScanHD_Array --force false \ #true: Disable various checks including chip types; false: otherwise. --keep-intermediate-data false \ #true: dump out intermediate data during apt processing; false: otherwise. --doDualNormalization true \ #true: quantile normalize CN and SNP separately; false: do not quantile normalize CN and SNP separately --adapter-type-normalization false \ #true: perform adapter type normalization; false: otherwise. Should be always set to "false" for CytoScanHD_Array as the adjustment has been incorporated in "signal-adjustment-covariates" --probe-file CytoScanHD_Array.probe_tab \ #specify the probe sequence file --run-geno-qc true \ #true: Run the GenoQC engine; false: otherwise --qca-file CytoScanHD_Array.r1.qca \ #if run-geno-qc is set to be true, it is required to provide this file --qcc-file CytoScanHD_Array.r1.qcc \ #if run-geno-qc is set to be true, it is required to provide this file --text-output false \ #true: Output data in ASCII text format in addition to calvin format; false: otherwise --cnchp-output false \ #true: report CNCHP file(s); false: otherwise. Either cnchp-output or cychp-output has to be true --cychp-output true \ #true: report CYCHP file(s); false: otherwise. Either cnchp-output or cychp-output has to be true --reference-output CnNewRef.REF_MODEL \ #specify name of the new copy number reference file with file extension "REF_MODEL" --cdf-file CytoScanHD_Array.cdf \ #specify the chp definition file --chrX-probes CytoScanHD_Array.chrXprobes \ #specify the chrX probe file --chrY-probes CytoScanHD_Array.chrYprobes \ #specify the chrY probe file --annotation-file CytoScanHD_Array.na32.annot.db \ #specify the NetAffx database file --male-gender-ratio-cutoff 1.5 \ #male gender call threshold for chrX/Y ratio gender calling --female-gender-ratio-cutoff 0.9 \ #female gender call threshold for chrX/Y ratio gender calling --xx-cutoff 0.61 \ #lower limit of the gender call threshold for hasXX gender call --xx-cutoff-high 0.95 \ #upper limit of the gender call threshold for hasXX gender call --y-cutoff 0.58 \ #gender call threshold for hasY gender call --out-dir output_dir \ #specify the output directory --covariates-file CytoScanHD_Array.hg19.v3.refcovar \ #specify the covariate file that contains probeset-based covariate(s) that doesn't exist in the annotation db file --signal-adjustment-covariates covariate-signal-adjuster.\ #covariate-signal adjuster order=fragment-adapter-type,fragment-length.\ #the covariates to be used in the order in which they are to be applied bin-type=discrete,equally-populated.\ #ordered list correspoinding to each covariate controls whether the covariate is treated directly as discrete variable, or as a continuous variable (equally-populated or equally-spaced) bin-count=0,100 \ #ordered list corresponding to each covariate controls how a continuous variable is discretized into bins. Must be 0 for discrete covariates --lr-adjustment-covariates covariate-lr-adjuster.\ #covariate log2 ratios adjuster order=SuperGC,median-signal,marker-class.\ #the covariates to be used in the order in which they are to be applied bin-type=discrete,equally-populated,discrete.\ #ordered list correspoinding to each covariate controls whether the covariate is treated directly as discrete variable, or as a continuous variable (equally-populated or equally-spaced) bin-count=0,100,0.\ #ordered list corresponding to each covariate controls how a continuous variable is discretized into bins. Must be 0 for discrete covariates iqr-scaling=on,on,on.\ #ordered list corresponding to each covariate on scales IQR for each bin to be equal subtract-from-XY=on,off,on \ #ordered list corresponding to each covariate. “on” applies covariate adjustment to ChrX,ChrY markers. --wave-correction-reference-method wave-correction-reference-method.\ #estimate waves using the reference samples trim=2.0.\ #trim parameter for absolute adjusted log2 ratios after each wave percentile=0.75.\ #percentile to use for each probeset in finding wave. E.g., 0.75 means 75-th percentile. wave-count=6.\ #number of waves to calculate demean=false \ #true: demean prior to finding each wave; false: otherwise --local-gc-background-correction-reference-method none \ #should be always set to "none" for CytoScanHD_Array --local-gc-background-intensity-adjustment-method none \ #should be always set to "none" for CytoScanHD_Array --image-correction-intensity-adjustment-method none \ #should be always set to "none" for CytoScanHD_Array --cel-files CELFileList.txt #an ASCII file that contains the full path of input CEL files for reference creation, where the first row of the file is "cel_files" and each subsequent row corresponds to each CEL file
A command to run analysis workflow using the reference built in the command above for CytoScanHD will look like the following below (note that this would have to be edited to remove all comments starting with #). If no analysis modules are specified in the command all will be run by default and if any are specified then only those specified are run. We strongly recommend that you explicitly specify all parameters in either a script or a xml-file that is in approved ChASParam format.
apt-copynumber-cyto -v 4 \ #verbose output level in the log file ranging from 1 (least details) to 4 (most details) --cyto2 false \ #true: Cytogenetics_Array; false: CytoScanHD_Array --doDualNormalization true \ #true: quantile normalize CN and SNP separately; false: do not quantile normalize CN and SNP separately --keep-intermediate-data false \ #true: dump out intermediate data during apt processing; false: otherwise. --run-geno-qc true \ #true: Run the GenoQC engine; false: otherwise --qca-file CytoScanHD_Array.r1.qca \ #if run-geno-qc is set to be true, it is required to provide this file --qcc-file CytoScanHD_Array.r1.qcc \ #if run-geno-qc is set to be true, it is required to provide this file --snp-qc-use-contrast true \ #only used by 2.7MCytogenetics_Array, will be ignored by CytoScanHD_Array --snp-qc-snp-list CytoScanHD_Array.snplist.txt \ #specify the snp list to compute the processed SNPQC and Raw SNPQC. If it is not specified, apt uses all SNPs. --force true \ #true: Disable various checks including chip types; false: otherwise. --adapter-type-normalization false \ #true: perform adapter type normalization; false: otherwise. Should be always set to "false" for CytoScanHD_Array as the adjustment has been incorporated in "signal-adjustment-covariates" --text-output false \ #true: Output data in ASCII text format in addition to calvin format; false: otherwise --cnchp-output false \ #true: report CNCHP file(s); false: otherwise. Either cnchp-output or cychp-output has to be true --cychp-output true \ #true: report CYCHP file(s); false: otherwise. Either cnchp-output or cychp-output has to be true --set-analysis-name cyhd \ #Analysis name to use as prefix for output files. The official name for CytoScanHD_Array is cyhd. --cdf-file $LIBDIR/CytoScanHD_Array.cdf \ #specify the chp definition file --chrX-probes CytoScanHD_Array.chrXprobes \ #specify the chrX probe file --chrY-probes CytoScanHD_Array.chrYprobes \ #specify the chrY probe file --annotation-file CytoScanHD_Array.na32.annot.db \ #specify the NetAffx database file --reference-input CytoScanHD_Array.na32.v3.REF_MODEL \ #specify the copy number reference to use --out-dir output_dir \ #specify the output directory --male-gender-ratio-cutoff 1.5 \ #male gender call threshold for chrX/Y ratio gender calling --female-gender-ratio-cutoff 0.9 \ #female gender call threshold for chrX/Y ratio gender calling --xx-cutoff 0.61 \ #lower limit of the gender call threshold for hasXX gender call --xx-cutoff-high 0.95 \ #upper limit of the gender call threshold for hasXX gender call --y-cutoff 0.58 \ #gender call threshold for hasY gender call --local-gc-background-intensity-adjustment-method none \ #should be always set to "none" for CytoScanHD_Array --image-correction-intensity-adjustment-method none \ #should be always set to "none" for CytoScanHD_Array --wave-correction-log2ratio-adjustment-method wave-correction-log2ratio-adjustment-method.\ #apply wave correction bandwidth=101.\ #used in non-parametric wave smoothing bin-count=25.\ #used in non-parametric wave smoothing wave-count=6.\ #must be less than or equal to the number of waves specified in wave-correction-reference-method wave-smooth=true \ #true: apply additional non-parametric wave smoothing; false: otherwise. --cn-calibrate-parameters calibrated-log2ratios.\ #specify parameters to compute calibrated log2 ratios alpha-cn-calibrate=0.564278.\ #calibrated alpha for autosomes alpha-X-cn-calibrate=0.619453.\ #calibrated alpha for Chr X alpha-Y-cn-calibrate=0.494620.\ #calibrated alpha for Chr Y beta-cn-calibrate=1.\ #calibrated beta for autosomes beta-X-cn-calibrate=1.\ #calibrated beta for Chr X beta-Y-cn-calibrate=1 \ #calibrated beta for Chr Y --analysis genotype \ #generate genotype calls for genotypable SNPs and the genotype calls are used by LOH analysis module. Should always specify this for CytoScanHD_Array. --analysis log2-ratio.\ #log2 ratio calculation analysis module gc-correction=false.\ #true: apply gc-correction; false: otherwise. Should aways set it to be false for CytoScanHD_Array as it has done by covariate adjuster module. median-autosome-median-normalization=true.\ #true: apply median autosome median correction; false: otherwise. median-smooth-marker-count=5 \ #running median marker count for weighted log2 ratio. It is ignored by CytoScanHD_Array, only for Cytogenetics_Array. --log2ratio-adjustment-method log2ratio-adjustment-method-high-pass-filter.\ #high pass filter log2 ratio adjustment analysis module use=true \ #true: use this module for the analysis; false: otherwise. --analysis allelic-difference-CytoScan.\ #allelic peak calculation module outlier-trim=3.0.\ #trim input allelic differences to be 3 or -3 if they go beyond those limits. step=20.\ #step size for another density estimation across the genome window=100.\ #number of SNPs used by the kernel density estimator point-count=128.\ #number of output grids for the kernel density estimator bandwidth=0.25.\ #adjustment to the data-adaptive bandwidth for the kernel density estimator. Must be 0 < bandwidth <= 1. cutoff=0.05.\ #parameter to remove density peaks that are likely due to noise clean-threshold=0.35.\ #controls with noisy markers are removed from the visualization because they are indeterminately far from adjacent peaks. symmetry=true \ #true: the data is mirrored about the X axis before fitting the density curves; false: otherwise. --analysis kernel-smooth.\ #apply kernel smooth to the log2 ratios sigma_span=50 \ #bandwidth parameter for Gaussian smooth --analysis cn-cyto2.\ #Hidden Markove Model (HMM) analysis module hmmCN_state=\'0,1,2,3,4\'.\ #supported CN states for autosome hmmCN_mu=\'-2,-0.45,0,0.3,0.51\'\.\ #HMM state means for autosome hmmCN_sigma=\'0.35,0.35,0.25,0.25,0.25\'.\ #HMM state sigmas for autosome hmmCN_state-X=\'0,1,2,3,4\'.\ #supported CN states for Chr X hmmCN_mu-X=\'-2,-0.47,0,0.33,0.53\'\.\ #HMM state means for Chr X hmmCN_sigma-X=\'0.35,0.35,0.25,0.25,0.25\'.\ #HMM state sigmas for Chr X hmmCN_state-Y=\'0,1,2,3,4\'.\ #supported CN states for Chr Y hmmCN_mu-Y=\'-2,-0.45,0,0.3,0.51\'\.\ #HMM state means for Chr Y hmmCN_sigma-Y=\'0.35,0.35,0.25,0.25,0.25\'.\ #HMM state sigmas for Chr Y diagonal-weight-Y=0.995.\ #transition probability matrix diagnal for Chr Y mapd-weight-Y=0.\ #per sample adjustment parameter to HMM state sigmas using MAPD for Chr Y min-segment-size-Y=5.\ #require min segment size (number of markers) for Chr Y hmm-confidence-weight-Y=0.6.\ #parameter for HMM confidence for Chr Y diagonal-weight=0.995.\ #transition probability matrix diagnal for autosome mapd-weight=0.\ #per sample adjustment parameter to HMM state sigmas using MAPD for autosome min-segment-size=5.\ #require min segment size (number of markers) for autosome hmm-confidence-weight=0.6.\ #parameter for HMM confidence for autosome diagonal-weight-X=0.995.\ #transition probability matrix diagnal for Chr X mapd-weight-X=0.\ #per sample adjustment parameter to HMM state sigmas using MAPD for Chr X min-segment-size-X=5.\ #require min segment size (number of markers) for Chr X, except for the par regions hmm-confidence-weight-X=0.6.\ #parameter for HMM confidence for Chr X shrink=true \ #true: apply wavelet shrinkage to the log2 ratio before HMM calls; false: otherwise --analysis cn-cyto2-gender.\ #Y-Gender call analysis module cutoff=0.5 \ #cutoff threshold for Y-Gender call --analysis cn-segment \ #generate HMM copy number call segment table. Should always specify this for CytoScanHD_Array. --analysis lohCytoScan.\ #LOH analysis module for CytoScanHD_Array lohCS_errorrate=0.05.\ #control error rate for LOH algorithm lohCS_beta=0.001.\ #parameter for LOH algorithm lohCS_alpha=0.01.\ #parameter for LOH algorithm lohCS_separation=1000000.\ #LOH separation parameter for LOH algorithm lohCS_nMinMarkers=10.\ #Minimum marker count for LOH algorithm lohCS_NoCallThreshold=0.05.\ #No call threshold for LOH algorithm lohCS_minGenomicSpan=1000000 \ #Minimum genomic span for LOH algorithm --analysis loh-segment \ #generate LOH call segment table. Should always specify this for CytoScanHD_Array. --analysis cn-neutral-loh \ #generate copy neutral LOH segment table. Should always specify this for CytoScanHD_Array. --cel-files CELFileList.txt #an ASCII file that contains the full path of input CEL files for single sample mode processing, where the first row of the file is "cel_files" and each subsequent row corresponds to each CEL file
WARNING: apt-copynumber-cyto will overwrite any existing output files it finds. If you wish to keep existing results make sure to specify a different output directory name.
NOTE: On windows the DOS prompt does not support wildcard expansion and the preferred method is to supply a text file with the path to the cel files via the '--cel-files' option (see below for details of file format).
NOTE: The windows DOS prompt also does not allow a continuation of a command with the '\' character, unlike unix. So in the examples shown here the '\' character should be omitted and everything entered on a single line.
As a performance estimate, running the 270 Hapmap samples on local disk on a 8 processor 2GHz Dual-Core AMD Opteron Processor 870 with 16G of RAM on a 64-bit linux OS took 801 minutes. RAM usage was 14 GB memory.
apt-copynumber-cyto - A program to compute copy number
results from DNA analysis arrays.
sample usage for CytoScanHD:
./apt-copynumber-cyto \
--verbose 3 \
--cyto2 false \
--run-geno-qc true \
--qca-file ./lib/CytoScanHD_Array.r1.qca \
--qcc-file ./lib/CytoScanHD_Array.r1.qcc \
--cychp-output true \
--cnchp-output false \
--text-output false \
--reference-input ./lib/CytoScanHD_Array.na32.v3.REF_MODEL \
--cdf-file ./lib/CytoScanHD_Array.cdf \
--chrX-probes ./lib/CytoScanHD_Array.chrXprobes \
--chrY-probes ./lib/CytoScanHD_Array.chrYprobes \
--annotation-file ./lib/CytoScanHD_Array.na32.annot.db \
--out-dir ./output/CytoScaHD_cels \
./cel/NA02571_A10_Baseline_CytoScanHD_VH_20101103.CEL
sample usage for Cytogenetics_Array:
./apt-copynumber-cyto \
--verbose 3 \
--cyto2 true \
--run-geno-qc false \
--cychp-output true \
--cnchp-output false \
--text-output false \
--reference-input ./lib/Cytogenetics_Array.na32.v1.REF_MODEL \
--cdf-file ./lib/Cytogenetics_Array.cdf \
--chrX-probes ./lib/Cytogenetics_Array.chrXprobes \
--chrY-probes ./lib/Cytogenetics_Array.chrYprobes \
--annotation-file ./lib/Cytogenetics_Array.na32.annot.db \
--out-dir ./output/Cytogenetics_Array_cels \
./cel/HapMap-As_NA18547_A08_01_NN_20081218.CEL
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 '']
Input Options
--chipstream String representing chipstream parameters.
This includes normal-diploid analysis
parameters . [default 'chipstream']
--check-input-files Does an upfront check of the syntax and
content of the input files:
gender-override, genotype-call-override,
snp-reference-input files. [default 'true']
--doDualNormalization The usual default action is to normalize
SNP and CN probeset separately. This option
allows a single normalization set for
CytoScanHD chips. [default 'true']
--config-file The configuration file name as passed from
GTC or the Cyto Browser. [default '']
--antigenomic-probe-file The probe indexes (ProbeID - 1) of the
antigenomic probes on the array. [default
'']
--snp-reference-input-file Input SNP reference file name. [default '']
--reference-input Input reference file name. [default '']
--probe-file File defining probe sequences and
locations. [default '']
--cdf-file File defining probe sets. [default '']
--spf-file spf format file defining probe sets.
[default '']
--qcc-file File defining QC probesets. [default '']
--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. [default '']
--chrY-probes File containing probe_id (1-based) of
probes on chrY. Used for copy number probe
chrX/Y ratio gender calling. [default '']
--normal-diploid-files-file Text file specifying normal-diploid
probeset files. First line must be
'normal_diploid_files'. [default '']
--reference-cels 'Normal' CEL file(s) to process when doing
paired analysis of Cancer vs. Normal.
[default '']
--annotation-file NetAffx Annotation database file. [default
'']
--normal-diploid-files Normal Diploid probeset file names.
[default '']
--sketch-size The number number of point to be used for a
sketch. [default '50000']
--covariates-file External covariates file. [default '']
--minSegSeparation Value used to skip over centromere in LOH.
[default '1000000000']
Output Options
--snp-reference-output-file Output SNP reference file name. [default
'']
--reference-output Output reference file name. [default '']
--file-name-prefix CYCHP file name prefix. [default '']
--file-name-suffix CYCHP file name suffix. [default '']
--file-name-ext CYCHP file name extension. [default
'cychp']
Analysis Options
--run-geno-qc Run the GenoQC engine. [default 'false']
--adapter-type-normalization Adapter Type Normalization option. true =
perform adapter type normalization.
[default 'false']
--signal-adjustment-covariates Covariate-based signal adjustment. [default
'']
--lr-adjustment-covariates Covariate-based log ratio adjustment.
[default '']
-a, --analysis String representing analysis pathway
desired. [default '']
--wave-correction-reference-method String representing wave correction pathway
desired. [default '']
--local-gc-background-correction-reference-method String representing local gc correction
background pathway desired. [default
'none']
--local-gc-background-intensity-adjustment-method String representing local gc correction
background intensity adjustment pathway
desired. [default '']
--image-correction-intensity-adjustment-method String representing image correction
intensity adjustment pathway desired.
[default '']
--log2ratio-adjustment-method String representing high pass filter
parameters for modification of log2ratios.
[default '']
--wave-correction-log2ratio-adjustment-method String representing wave correction
log2ratio adjustment pathway desired.
[default '']
--allele-peaks-reporter-method String representing allele peaks reporter
pathway desired. [default
'allele-peaks-reporter-method']
--hmm-priors Read HMM priors from the reference file.
[default 'false']
--hmm-means-check Check HMM priors in the reference file for
consistency. [default 'false']
--brlmmp-parameters Parameters to use when running brlmmp.
[default '']
QC Options
--snp-qc-use-contrast SNP QC use intensity contrast. [default
'false']
--snp-qc-snp-list Input file containing a list of SNP Ids to
be used in calculating the SNPQC value.
[default '']
--snp-qc-k SNP QC K value. [default '2.0']
--snp-qc-em-threshold SNP QC EM Threshold. [default '0.05']
--snp-qc-bin-size SNP QC bin size. [default '0.04']
Misc Options
--explain Explain a particular operation (i.e.
--explain cn-state or --explain loh).
[default '']
Advanced Options
--probeset-ids Tab delimited file with column
'probeset_id' specifying probesets to
summarize. [default '']
--global-parameter-override Global parameters in loh-cyto analysis
input string will override those given in
the snp-reference-input-file. [default
'false']
--keep-temp-reference-data Set to true, this option will keep the
final signal and intensity values computed
while determining the CN reference file.
Warning: It may be large. [default 'false']
--keep-intermediate-data Set to true, this option will keep all,
intensity values computed while invoking
any intensity adjustment method. [default
'false']
--keep-intermediate-data-local Set to true, this option will keep all,
intensity values computed while invoking
any intensity adjustment method. This is a
duplicate option for local testing.
[default 'false']
--genotype-call-override-file Input file containing genotype calls to be
used in place of brlmmp-p calls. [default
'']
--gender-override-file A file containing externally computed
genders. It is used in reference and
snp-reference generation [default '']
--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 for GC content.
[default '25']
--xChromosome X Chromosome [default '24']
--yChromosome Y Chromosome [default '25']
--male-gender-ratio-cutoff Male gender ratio cutoff [default '1.3']
--female-gender-ratio-cutoff Female gender ratio cutoff [default '1.0']
--reference-chromosome Reference chromosome [default '2']
--xx-cutoff XX cutoff [default '0.8']
--xx-cutoff-high XX cutoff high [default '1.07']
--y-cutoff Y cutoff [default '0.65']
--warning-message-limit Set the limit on the number of warning
message produced. [default '10']
--waviness-block-size marker count [default '50']
--waviness-genomic-span genomic segment length [default '0']
--cn-calibrate-parameters SmoothSignal calibration parameters
[default '']
Engine Options (Not used on command line)
--cels CEL files to process. [default '']
--arrs ARR files to process. Must be paired with
cels. [default '']
--result-files CYCHP files to output. Must be paired with
cels. [default '']
Additional CNAnalysisEngine Options
--geno-qc-file The file output from GenoQC. [default '']
--cyto2 Processing CYTO2 chip. [default 'false']
--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']
--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 '']
Data transformations:
pdnn-reference-method CopyNumber PDNN
wave-correction-reference-methodCopyNumber WaveCorrection
additional-waves-reference-methodCopyNumber AdditionalWaves
pdnn-intensity-adjustment-methodCopynumber PDNN Intensity
Adjustment
high-pass-filter-intensity-adjustment-methodCopyNumber
HighPassFilter
wave-correction-log2ratio-adjustment-methodCopynumber Wave
Correction Log2Ratio Adjustment
log2ratio-adjustment-method-high-pass-filterCopyNumber
HighPassFilter Log2Ratio Adjustment
cn-state CopyNumber CNState
cn-cyto2 CopyNumber CNCyto2
log2-ratio Copynumber Log2Ratio
log2-ratio-cyto2 Copynumber Log2RatioCyto2
allelic-difference Copynumber AllelicDifference
allelic-difference-CytoScanCopynumber AllelicDifference CytoScan
gaussian-smooth CopyNumber GaussianSmooth
genotype Genotype
kernel-smooth CopyNumber KernelSmooth
loh CopyNumber LOH
loh-cyto2 CopyNumber LOH Cyto2
lohCytoScan CopyNumber LOH CytoScan
cn-neutral-loh Copynumber CNNeutralLOH
normal-diploid Copynumber NormalDiploid
mosaicism Copynumber Mosaicism
cn-gender Copynumber CNGender
cn-cyto2-gender Copynumber CNCyto2Gender
cn-segment Copynumber SegmentCN
loh-segment Copynumber SegmentLOH
allele-peaks Copynumber AllelePeaks
chipstream Copynumber Chipstream
covariate-signal-adjusterCovariate Signal Adjuster
covariate-lr-adjuster Covariate log2ratio Adjuster
Q. Does apt-copynumber-cyto support the whole genome SNP6 chips.
A. No. For SNP6 use apt-copynumber-workflow.
1.7.1