Import UNNAMED (Blank is a delimiter) UNNAMED (Parse from left) Additional New Design Variable Names Affection Status Coding Allele Delimiter Allele Peaks Data Set Alleles to Use for Genotypes Allocate Memory Size Alternate Phenotype File Annotated Variants within Known Genes (gene) Annotation Columns Annotation Data Set Annotation File Annotation Merge Variables Annotation SAS Data Set Apply log2 transformation to intensities Apply original column names ArrayTrack Annotation Output Data Set ASM Files from Version of Assembly Pipeline prior to 2.0 Background Correction Background Correction Method Background Subtraction Baseline Reference Data Set Baseline Reference SAS Data Set Baseline Variable BIM File Bin Method Bin Size Bin Summary Statistic Binary PED File Binding Density QC By Variables Cast Selected Columns into Roles Cel Layout File CGA Tools testvariants File Channel Status Check available disk space Check uniqueness of column names Choose a folder containing files listed in the File column Chromosome Chromosome Summary Data Set Chromosome Variable CN Columns to Include CN Measurements to Include (100K or 500K Arrays) Code genotypes numerically Column Delimiter Column Delimiter for Genotype Probability File(s) Columns to Include Columns to Include In Output Data Set Compress output data sets Compute Reference Scaling Factor Continuous Variables to Summarize Copy Number Annotation Data Set Copy Number Annotation SAS Data Set Copy Number Data Set Copy Number File Count Data Count of Variations by Gene (geneVarSummary) Count reads by strand Covariate File Covariate File has a Header Row Create Combined Data Set Create Final Report Data Set Create Quality Flag Data Set Create separate data sets for B_Allele_Freq and/or Log_R_Ratio Create separate data set(s) for each chromosome when there are more variants than: Create separate data sets for each selected measurement Create separate data sets for SNP- and CN-summarized probesets Create wide Output Genotype Data Sets Cross Type Custom File Filter Expression Customer Array Cut-off for DP Cut-off for GQ Data File Data File Type Data Set Containing Probes to Remove Data Start Row Data Step Statements Delimiters Detection p-Value Cutoff for Setting Individual Intensities to Missing Display marker genotype cell color plots Drop SNPs with this percentage of samples that are below: Encoding of Raw Array Files End Exclude rows with missing physical position Exon Count Exon Ends Exon Starts Experimental Design Data Set Corresponding to Baseline Reference Data Set Experimental Design File Experimental Design SAS Data Set Corresponding to Baseline Reference SAS Data Set Exponential Multiplier of Kernel Density Expression FAM File Feature Identifier Feature Identifier for Computing Counts File Filter Expression File Type Files for Variants Call Files in PBAT Format Files to Import Filter before: Filter out genes with detection p-value above: Filter to Include Annotation Rows Filter to Include Gene Model Rows Filter to Include Markers Filter to Include Observations Flag Filter Expression Folder Containing a FASTA-formatted Reference Sequence Folder Containing Other Library Files Folder Containing Raw Data Files Folder Containing Rterm.exe Folder Containing the BPMAP Files Folder Containing the CDF File Folder Containing the Library Files Folder Containing the Meta Probeset File Folder Containing the RCC Data Files Folder of BAM Files Folder of Data Files from Eland Folder of Illumina Data File Folder of Input Files Folder of Raw Array Files Folder of Raw BAM Data Files Folder of Raw Data Files Folder of Raw Files Folder of Raw SAM Data Files Folder of Samples File Folder of SNP/DIP Detection Table CSV Files Folder of Track Gene Text Settings Files Folder of VCF Files ...for at least this percentage of the samples GC Score Cutoff Gene Identifier Gene Model Text File Genotype Data Set Genotype File Genotype Files Genotype Probability File(s) Genotype Probability Threshold Genotyping Calls Data Set Genotyping Error Threshold Get all column names from first row Get Breadth of Coverage How shall I get the information about your experiment ID Variables ID Variables to Keep Illumina Data File Imaging QC Import CEL intensities without merging annotation Individual Variables Input Data Set Input SAS Data Set Include intron bins Include MM in output Include sequence data in output Indicator of Different Column Names across Raw Data Files Input Arlequin File Input NEXUS File Input OneMap File Input Pedigree File Input Phenotype File Input SAS Data Set Input WinQTLCart File Intensity Variables to Bin Keep single probes not associated to any probeset Keep single-probe-sets not associated to any transcript cluster Key Variable(s) to Merge with Input Data Set Key Variable(s) to Merge with Input SAS Data Set Length of Sample ID Column LGEN File List of Phenotype Variable Names List of Variable Names List of Variable Names and Lengths List of Variable Names and Types List-Style Specification of Individual Variables List-Style Specification of Intensity Variables to Bin List-Style Specification of Marker Variables List-Style Specification of Trait Variables List-Style Specification of Variables to be Included for Normalization LOH Columns to Include LOH Measurements to Include (100K or 500K Arrays) Map Data Set Map File MAP Files Marker Data Set Marker ID Variable Marker Label Marker Name Variable Marker Type Marker Variables Master Variations (masterVarBeta) Maximum Column Length Maximum Intron Bin Size Measures to Include (Chromosomes Data) Measures to Include (CopyNumber Data) Measures to Include (SNP6 Array) Merge Variables Meta Probeset File MiniML-formatted File Minimum Number of Columns to Scan Minimum Number of Probes to Summarize Probe-Set Level Missing Covariate Value Missing Genotype Value Missing Individuals Threshold Missing Phenotype Value Missing Quantitative Trait Value Name of Phenotype Variable Names of Variables Preceding Genotype Probability Columns NBeads Output Data Set New Study New Variable Names for Experimental Design No Family ID Column No Parent ID Columns No Phenotype Column No Sex Column Normalization Normalize copy number data using autosomes Normalize SNP data using autosomes Number of CEL Files to Process at a Time Number of Channels in Each File Number of Data Files to Process at a Time Number of Genotype Probability Columns Number of Genotype Probability Columns per Individual Number of Rows in Each Bin Number of Rows to Scan Include SNP variants only Options Order Annotation Data Set by SNP column order Output Allele Intensity Data Set Output Allele Intensity Experimental Design Data Set Output Annotation Data Set Output Copy Number Intensity Data Set Output Data Set Output Data Set Name Output Data Set of Normalization Factors Output Expected Genotype Data Set Output Experimental Design Data Set Output File Name Output File Prefix Output Folder Output Genotype by Chromosomes Output Genotype Data Set Output Genotype Probabilities Data Set Output Genotype Threshold Data Set Output Map Data Set Output Probe-level Intensity Data Set Output Sequence Data Set Output SNP-summarized Copy Number Intensity Data Set p-Value Cutoff for Segregation Test Package or Individual Genome Folder Containing ASM Results Parent 1 ID Variable Parent 2 ID Variable Parse Associated Gene Column PDF or RTF Output File PDF Output File PDF Output File Name PED or FAM Files Pedigree File Percentage of Data to Be Included in Training Data Percentage of Samples Below Cut-off(s) for Dropping SNPs Percentage of samples for dropping SNPs Perform log2 transform Phenotype File has a Header Row Ploidy Level Ploidy Type PM Correction Position Position Variable Positive Control Limit of Detection QC Positive Control Linearity QC Positive Control Method Prefix for New Columns Prefix for Output Data Set Names Prefix for Output Experimental Design Data Set Names Prefix for SNP Names Prefix to Append to SNP Column Names Prefix to Append to SNP Column Names (for Full Data Table) Prefixes of SNPs to Include in Data Sets Probe Coordinates Output Data Set Probe Group File Probe Normalization Probe Normalization Method Probeset Variable Probe Variable Probeset File QC Control File QC Output Data Set QC Probe Output Data Set Quality Flag Output Data Set Quantitative Variables Reference File Remove AFFX Control SNPs from output data set(s) Remove PCR duplicates Row Number of Variable Names Sample File Sample File Sample Files Sample Variable SAS Code for Customized Flagging Rule SAS Code to Create Columns SAS Code to Create New Design Variables Save as SAS Data Set Scaling Factor SD Output Data Set Segments CN Data Set Segments CNNeutralLOH Data Set Segments LOH Data Set Segments Mosaicism Data Set Segments NormalDiploid Data Set Select an array Select Column to Parse Select Files Select key variable to merge files Select the folder containing .ARR files Select the folder containing pairs of ARR and data files Select the type of file(s) to input Selected Column Server Output Directory Set flagged data to missing Set heterozygous to missing Set individual genotypes to missing that are below: Shifting Factor Smoothing Bandwidth Multiplier SNP Annotation Data Set SNP Annotation SAS Data Set SNP Map File Sort genotype columns and map rows Source of Files Specify the maximum number of missing genotypes for a locus to be included in the output data set Specify your Input File Spot Coordinates Output Data Set Start Strand Study Summarization Method Summary Level Summary Method Tab-Formatted Probe Sequence File Track Gene Text Setting File Trait Variables Transformation Method Type of Array Type of File Type of File(s) Type of File Conversion Type of Map Files Type of Other Files Type of PED/FAM and Other Files Type of Phenotype Variable Unit for Genetic Distance Value of Chromosome Variable Indicating Non-autosomes Value of Columns Above to Be Associated with Non-autosomes Variables By Which to Merge Annotation Data Variables Containing Primary Data Variables to be Included for Normalization Variables to Keep in Output Data Set Variations (var) Variations at Known db SNP Loci (dbSNPAnnotated) Weighted with Kernel Density What kind of data files do you have What type of Experiment is this Width of Positional Bin