• Introduction to Ion Reporter Software
  • About Ion Reporter Software
  • Ion AmpliSeq panel types
  • hg19 and GRCh38 human genome references
    • Requirements for GRCh38 custom BED file
  • Network and password security requirements
    • Network configuration and security
    • Password security
• Get started with Ion Reporter Software
  • Purchasing and ecommerce
    • Create a Thermo Fisher account
  • Ion Reporter Software on Thermo Fisher Connect Platform
    • Ion Reporter Software storage
    • Create an organization on Ion Reporter Software on Thermo Fisher Connect Platform
    • Invite a user to an organization on Connect
    • Sign in to Ion Reporter Software on Thermo Fisher Connect Platform
    • Join an existing Ion Reporter Software organization on Connect
  • Ion Reporter Server
    • Create an organization on Ion Reporter Server
    • Sign in to Ion Reporter Software on Ion Reporter Server
    • User roles and permissions
  • Ion Reporter Software dashboard
  • View notifications
  • Status alert emails
  • Troubleshoot sign ins and provide feedback for Ion Reporter Software
    • What can I do if I am locked out of my account?
    • How can I provide feedback?
    • How do I contact support if I have additional questions?
    • What special characters are allowed in names?
  • Set default number of rows displayed in tables
  • IonReporterUploader command-line utility
    • Download IonReporterUploader command-line utility
    • Run IonReporterUploader command-line utility
• Import and manage samples
  • Samples tab overview
  • Sample attributes overview
    • View sample attributes
    • Sample attributes
      • Gender attribute
    • Sample presets
      • Create a custom sample attribute
      • Sort the Sample Presets table
  • Sample import options
    • Automatic transfers of sequencing run data
    • Upload a BAM file to create a sample or samples
    • Upload a VCF file to create a sample
    • IonReporterUploader command-line utility
    • Import samples from Torrent Suite Dx Software
  • Sample definition
    • Define a sample manually
      • Define samples with one or more BAM files
      • Define a single VCF file as a sample
      • Define samples with a CSV file
    • Create a sample CSV file to define samples
    • Define samples as no-template controls
    • Edit a sample
    • Edit a sample used in an analysis
    • Lock a sample
  • Find samples
    • Search for samples
    • Sort the Samples table
    • Filter samples
    • Remove filters
  • Customize the Samples table
    • Add attributes to the Samples table
    • Create a Samples table preference
    • Rearrange columns in the Samples table
    • Apply a preference to the Samples table
    • Delete a Samples table preference
    • Restore table preference default settings
  • Transfer samples to users in other organizations
    • Transfer a sample to users in another organization
    • Transfer multiple samples to a user in another organization
    • Accept a sample from a user in another organization
  • Archive samples to an external storage device
  • Restore archived samples from an external device to Ion Reporter Server
  • Delete a sample
• Manage analysis workflows
  • About analysis workflows
  • Workflow tab overview
  • Find analysis workflows
    • Search for analysis workflows
    • Sort the Workflows table
    • Filter analysis workflows
    • Remove filters
  • View analysis workflow details
    • Analysis workflow details
  • Predefined analysis workflows
    • Tumor-normal pair research
      • Flow Space Alternate Allele Calculation (FAO) calculation
    • CNV and aneuploidy detection
  • Custom analysis workflows
    • Create a custom analysis workflow from an existing analysis workflow
    • Create a custom analysis workflow without predefined settings
    • Create a custom analysis workflow for use with Ion AmpliSeq HD panels
      • Analysis workflow templates for Ion AmpliSeq HD
    • Create a custom analysis workflow for use with Metagenomics research application
      • Custom primer sequences for Metagenomics analysis workflows
    • Enable tumor mutational burden calculation in existing analysis workflows
      • Reduce the impact of deamination in low-quality FFPEs
        • Customize an Oncomine Tumor Mutation Load - w3.1 - DNA - Single Sample analysis workflow
    • Custom analysis workflows for aneuploidy research
      • Create a custom analysis workflow for mosaicism, No Gender, or different tile sizes
      • Improve detection of small segmental CNV events
    • Transfer a custom analysis workflow
    • Edit a custom analysis workflow
  • Customize tuning parameters
    • Annotation parameters
    • Bamstats parameters
    • CNV Finding parameters
    • Fusions parameters
    • MSI parameters
    • Read Mapping parameters
    • Variant Finding parameters
    • Import custom variantCaller parameters
  • Steps in analysis workflow creation
    • Research applications
    • Sample groups
    • Add a filter chain to an analysis workflow
    • Import panel files from AmpliSeq.com
      • Generate an access code for AmpliSeq.com
    • Apply a copy number baseline workflow preset to an analysis workflow
    • Apply a sequence variant baseline workflow preset to an analysis workflow
    • Apply an exon tile fusion baseline workflow preset to an analysis workflow
    • Change the default filter chain for an analysis workflow
  • Workflow presets
    • Find workflow presets
      • Sort the workflows presets list
      • Search for workflow presets
      • Filter workflow presets
      • Remove filters
    • Custom annotation sources
      • Create annotation set workflow presets
      • View custom annotation sources
    • Create a final report template workflow preset
    • Copy Number Variant detection
      • VCIB baseline workflow presets
        • VCIB calculations
      • Create a copy number baseline workflow preset
      • Use gender to call gains from expected copy number changes
      • Create an analysis workflow that contains a copy number baseline
      • Augment an existing VCIB baseline workflow preset
    • Sequence variant baselines
      • Create a Sequence Variant Baseline workflow preset
    • Exon tile fusion baselines
      • Create an exon tile fusion baseline workflow preset
    • Upload a target regions BED file workflow preset
    • Upload a hotspots BED file workflow preset
  • Analysis workflow revision autonumbering
  • Lock an analysis workflow
• Analyses
  • About analyses
  • Analyses tab overview
  • Customize the Analyses table
    • Add attribute columns to the Analyses table
    • Change the order and width of columns in the Analyses table
    • Create an Analyses table preference
    • Apply an Analyses table preference
    • Restore default settings for the Analyses table
    • Delete an Analyses table preference
    • Analyses table column options
  • Find analyses
    • Search for analyses
    • Sort the Analyses table
    • Filter analyses
    • Remove filters
  • Launch an analysis
    • Demonstration samples
    • Manually launch an analysis
  • Launch analyses by batch
    • Batch launch analyses CSV file guidelines
  • Add an analysis note
    • View an analysis note
    • Search for an analysis note
    • Delete an analysis note
  • MyVariants
    • MyVariants table
    • MyVariants database
    • Classifications and Notes
    • Automatically add classifications and notes to variants
    • Apply flags, notes, or classifications to variants of interest
    • Search or filter the MyVariants table
    • Sort MyVariants
    • Edit a MyVariants database
    • Get the latest updates from the MyVariants database
    • View the variants in a MyVariants database
    • View a MyVariants database associated with an analysis workflow
    • Create a MyVariants database
    • Associate a MyVariants database with an analysis workflow
    • Export MyVariants database
    • Import MyVariants
    • Create a PDF report of MyVariants
  • Delete an analysis
  • Copy analyses to storage on Connect
    • Increase storage space on Connect
  • Monitor analyses
  • Reanalyze an aborted analysis
  • Share data from an analysis
    • Share analyses data
    • Unshare analyses data
    • Send an analysis to the Report role
  • Download BAM files
  • Download analysis files
  • Download detailed analysis logs
• Analysis results
  • Analysis Results table overview
  • Open and review analysis results
    • Display different views of analysis results
    • Hide or Unhide variants in Analysis Results list
    • Classify variants in analysis results
    • Apply a filter chain to analysis results
    • Show variants for a single chromosome
    • View notes attached to a variant
    • Add flag labels to variants of interest
    • Add a note to a variant
    • Locus View versus Allele View of variants
      • Locus View
      • Allele View
      • Allele subset information
    • Evaluate analysis results
      • Compare results of single or multiple analyses
    • View original source of annotation information
    • Links to external databases
    • Inactive links in the Analyses screen
  • Customize the Analysis Results table
    • Analysis Results table column options
    • Add attribute columns to the Analysis Results table
    • Change the order and width of columns in the Analysis Results table
    • Create an Analysis Results table preference
    • Apply an Analysis Results table preference
    • Delete an Analysis Results table preference
    • Restore default settings for the Analysis Results table
  • Edit Analysis Results
  • Variants file downloads
    • Download filtered variants
    • Download all variants
    • Download selected variants
  • Searches on the Analysis Results screen
  • CNV subtypes in the Analysis Results screen
  • Reasons for NOCALL in a gene-level CNV
  • CFTR analysis results
  • Allele calls for hotspot positions
  • RefGene GeneModel and Ensembl GeneModel transcript versions
  • Phred QUAL Score
  • Review analysis results for Ion AmpliSeq HD panels
  • View Oncomine BRCA analysis results
  • View Genomic Instability Metric (GIM) in analysis results
  • Immune repertoire analysis results
    • View immune repertoire analysis results
      • Sample results for immune repertoire
        • Spectratyping plots
          • Adjust data and access clone details in spectratyping plots
          • Example V-gene Mutation plots
          • V-gene usage and evenness plot examples
          • V-gene usage and Shannon Diversity plot example
          • V-gene usage and largest clone frequency plot example
          • V-gene usage and number of clones plot example
          • Spectratyping overview plot
          • Download spectratyping overview plots
        • V-gene usage
        • VJ‑gene usage heatmap
        • Clones detected per variable gene
        • CDR3 histogram
        • Somatic hypermutation profile
        • Isotype usage
      • QC Metrics for immune repertoire results
      • Clonal lineage identification
        • Clone Summary table
        • Download clone summary and lineage summary files
      • Compare the immune repertoire between samples
        • Example Jaccard Similarity Index for selected samples
        • Example correlation and proportion of shared clones
  • Microbiome health research analysis results
    • View microbiome health research analysis results
  • MSI analysis results
  • View tumor mutational burden analysis results
    • View the tumor mutational burden statistics
      • Example: Tumor Mutational Burden calculation
  • View Oncomine Myeloid Research Assay analysis results
  • View metagenomics analysis results
    • Reads included in Metagenomics analysis results
    • Reference output files for Metagenomics
    • Alpha-beta diversity results
    • Visualize OTU results with R-scripts graphs
    • View interactive taxonomy charts for metagenomics analyses
• Detailed analysis metrics
• Visualize analysis results with Ion Reporter Software
  • Genomic segmentation analysis results
    • Visualization of genomic segmentation analysis, Allele Specific Copy Number plots
  • Visualize HRR analysis results
  • Mutational Signature profiles
    • View the Mutational Signature Prediction report
    • Mutational Signature Prediction report
      • Mutation Signature Prediction report example
  • Time series visualizations
    • Create and view a time series graph
    • Example time series graphs
    • Example of dynamic edits to time series graphs
  • Set IRGV or IGV as the default viewer
  • Set IRGV preferences
  • Browse a visualization by amplicon name
  • Multiple analyses and multiple analysis types in IRGV
  • Visualize microbiome health research analysis results
  • Visualize aneuploidy analysis results
    • View single sample aneuploidy details
    • Change Y-axis height in Whole Genome aneuploidy visualization
    • Smoothing, no gender, and mosaicism results in IRGV
    • Visualization of triploid samples
  • Visualize the BRCA report
  • Adjust IRGV BAM tracks
  • Sort read coverage tracks by variant
  • CNV segment data in chromosome view
  • Visualize tumor mutational burden analysis results
    • Sample results
    • QC metrics for tumor mutational burden
  • Compare results of single or multiple analyses
    • Track order for non-aneuploidy analyses
  • Compare multiple analyses and download a TSV file
    • Venn diagram generation
  • Coverage histogram
  • Evaluate analysis results
    • Compare results of single or multiple analyses
    • Variants Table tab
    • Variant Matrix tab
    • IRGV & Generate Report tab
    • Variant Impact tab
    • CNV Heat Map tab
      • Filter impact on the variants displayed in heat maps
    • Gene Fusions tab
    • RNA Exon Variants tab
    • RNA Exon Tile Fusion Imbalance tab
    • Filter Options
      • Samples Venn diagram in Filter Options
      • Chromosome filter in the Filter Options
      • Filter Chains filter in the Filter Options
  • Novel fusion detection using expression imbalance
    • View RNA Exon Tile Fusion Imbalance plots
    • Example RNA Exon Tile Fusion Imbalance plots for a single analysis
    • Example RNA Exon Tile Fusion Imbalance read count plot for a single analysis
    • Example sample coverage plot for a single analysis positive for a fusion imbalance in NTRK1
    • Example RNA Exon Tile Fusion Imbalance call plot for multiple analyses
    • Example Normalized Read Depth by Gene RNA Exon Tile Fusion Imbalance plot for multiple analyses
    • Example Coverage Imbalance Scores plot
    • 3'/5' Imbalance scores for assay calls
      • View 3'/5' Imbalance scores
      • Interpret 3'/5' Imbalance scores for assay calls
        • Imbalance value calculation and predictions
          • Example plot for ALK driver gene
          • Example plot for RET driver gene
          • Example plot for ROS1 driver gene
        • Read number impact on calculation sensitivity
          • Sensitivity
          • High 5' expression
        • Normalized Detection Fractions (NDF)
        • Visualize and compare fusion results of multiple analyses with heatmaps
        • Example of an analysis with no fusions called
  • Visualize RNA exon variants
    • View RNA exon variants
    • Example RNA Exon Variant graph
  • Visualize variants in an analysis run with an Ion AmpliSeq HD analysis workflow
  • Visualize MSI analysis results
  • Visualize identified variants in an Oncomine analysis from a TagSeq analysis workflow
    • View analysis results for a single sample
    • Use filter chains to change analysis results
  • Visualize variants with IGV
    • Unidentified developer error in IGV on Macintosh computers
    • Unable to parse header in IGV
  • Visualization interpretation guidance
• Create and view reports
  • Final reports
    • View a published final report
    • Create a final report
    • Create a final report template from analysis results
    • Search for a final report template
    • Add a report template to an analysis workflow
    • Edit a final report template
    • Lock a report template
    • Delete a final report template
    • Generate a final report and approve with an electronic signature
  • Visualization reports
    • Create a visualization report
  • Amplicon coverage reports
    • View and filter an amplicon coverage report
    • Download an amplicon coverage report
      • Amplicon coverage report metrics
    • Open an amplicon coverage report in (IRGV)
  • Quality Control (QC) reports
    • View a Quality Control (QC) report
    • QC package coverage columns
    • Download Quality Control (QC) files
  • Available report sections
    • Quality Control (QC) metrics
    • Coverage Analysis metrics
    • Molecular Coverage Analysis metrics
  • Audit logs
    • View and download audit logs
    • View an audit log for a sample
    • View an audit log for a completed analysis
    • Download an audit log
• Filters and filter chains
  • About filters and filter chains
  • View filter chain details
  • Create a custom filter chain
  • Create a gene symbol filter
  • Edit a filter chain
  • Lock a custom filter chain in workflow presets
  • Delete a custom filter chain in workflow presets
  • Custom filter chain examples
    • Create an Expected Normal Ploidy Buffer filter chain
    • Create a gene symbol filter chain
    • Create a filter chain query
    • Create a MyVariants and Variant Classification filter chain
    • Create a COSMIC, ClinVar, MAF, and Variant Effect filter chain
    • Create a PValue, dbSNP, and Variant Type filter chain
  • Predefined filter chains
  • Predefined filters
    • Annotation source filters
      • 5000Exomes filters
      • Clinvar filter
      • COSMIC filter
      • dbSNP filter
      • DGV filter
      • DrugBank filter
      • ExAC filters
      • FATHMM Scores filter
      • Gene Ontology (GO) filter
      • Gene Symbol filter
      • gnomAD filters
      • Minor Allele Frequency filter
      • OMIM filter
      • Pfam filter
      • PhyloP Scores filter
      • UCSC Common SNPs filter
    • Data type filters
      • Allele frequency filter
      • Allele Ratio filter
      • Allele Read-Count filter
      • Alternate Allele Count filter
      • CNV Confidence Range filter
      • CNV Confidence Range—CNVs Only filter
      • CNV Somatic Confidence—CNVs Only filter
      • CNV Somatic Confidence Range filter
      • Confident Somatic Variants filter
      • Deamination filter
      • Default DNA and Fusions View filter
      • Default Fusions View filter
      • Disease Research Area (DRA) filter
      • Expected Normal Ploidy Buffer filter
      • Filtered Coverage filter
      • Functional Scores filter
      • Fusion Read Counts filter
      • Genetic Category Type filter
      • Genomic Coordinates filter
      • Homopolymer Length filter
      • Hotspot Genotype Allele filter
      • Hostpot Position Overlap filter
      • Location filter
      • Minimum Limit of Detection at Genomic Location filter
      • Minor Allele Frequency filter
      • MyVariants filter
      • Named Variants filter
      • Oncomine filter
      • Phred QUAL Score filter
      • Possible Polyploidy Alleles filter
      • PValue filter
      • Variant Classification filter
      • Variant Effect filter
      • Variant Subtype filter
      • Variant Type filter
      • Zygosity filter
• Annotation sources
  • Annotations available in Ion Reporter Software
    • Transcripts in REFSEQ and ENSEMBL canonical transcripts file
    • Contigs annotated in the GRCh38 reference genome
    • hg19 and GRCh38 dbsnp
  • Import a custom annotation source
    • Genomic region
    • Gene set
    • Transcript set
      • RefGene GeneModel and Ensembl GeneModel transcript versions
    • VariantDB files
  • Delete custom annotation sources
  • Change amino acid code
  • Variant identifiers for Oncomine panels
  • Oncomine Variant Annotator plugin
  • Preferred transcripts in default analysis workflows
    • Create annotation set without preferred transcript sets
  • Annotation sources and scores
    • Pfam annotations
  • Annotation versions and calculations
    • Polyphen-2
  • Codon differences in chromosome M
    • Background information
  • Effect of Ensembl and RefSeq sources on Polyphen and SIFT scores
  • Genetic Category Type variants
    • HasDeNovoNonRefAllele
    • HasDeNovoRefAllele
    • IsNewlyHomozygousNonRef
    • IsNewlyHomozygousRef
    • IsNewlyHeterozygousNonRef
    • InCompoundHeterozygote
    • InTransPhaseCompoundHeterozygote
    • HasMaleMaternalX
    • HasUnknownX
    • InconsistentWithFather
    • InconsistentWithMother
    • InconsistentWithParents
    • Gene Category Type and Variant Effect filter types can be applied to the same variants
    • Genetic Category Type and MAF filter
  • Grantham score
  • HGVS genomic codes
  • Ion Reporter Software references
    • Ambiguity codes for three positions on chromosome 3
    • Hard masked PAR regions in chromosome Y
    • Chromosome M
  • SIFT score
  • phyloP score
  • PolyPhen-2 score
  • phyloP
• Administer Ion Reporter Software
  • Admin tab overview
  • Manage users
    • Create user accounts on Ion Reporter Server
    • Modify the permissions of a user on Ion Reporter Server
    • Enable or disable private folders on Ion Reporter Server
    • Set or reset the password on a user account on Ion Reporter Server
    • Disable a user account on Ion Reporter Server
    • Delete a user account on Ion Reporter Server
  • Manage system services
  • View software version information
  • Manage archives
    • Archive analyses to an external storage device
    • Restore archived analyses and samples
  • Manage plugins
    • Download plugins from Connect
    • Install and uninstall plugins
  • Manage policies
    • Enable electronic signatures for final reports
    • Set password policies
  • Manage audit records
    • Download an audit trail of user activities
    • Download an audit log of system activities
    • Download an audit log for administrative policies
  • Reset the API token for Ion Reporter Software on Thermo Fisher Connect Platform
  • Reset the API token on Ion Reporter Server
• Troubleshooting
  • Software is unresponsive and cannot be rebooted
  • Custom BED file causes an error
• Fusion analyses
  • Fusion calls in analysis results
  • Analysis configuration file for gene fusion analysis
    • Edit the gene fusion analysis configuration file
    • Editable parameters in the analysis configuration file
  • Data types for gene fusions analyses
    • Process controls for TagSeq and Ion AmpliSeq HD research panels
    • Multiple fusions in the same gene
  • Fusion sample QC metrics
    • FusionSampleOverallCall
    • Total Mapped Fusion Panel Reads
    • Minimum Mean Read length
    • Minimum total mapped reads per pool
    • Minimum number of Valid pools
  • Fusion detection methods
    • Targeted fusion detection method
    • Non-targeted fusion detection method
    • Exon tiling fusion detection method
    • Barcode CrossTalk QC
    • Exon deletion thresholds for Oncomine Fusion panels
  • Confirm the presence of fusion calls in Ion Reporter Software
  • Filter chains for fusion panels
• Ion Reporter Software web services API
  • Check if analysis is running
  • Check if a sample exists
  • Download a BAM file
  • Download a file
  • Download QC and final reports
  • Get analysis details
    • Download all analyses with one call
    • Download analysis information
  • Get associated BAM files
  • Get available cancer types
  • Get available storage space
  • Get current results TSV file
  • Get data upload path with authentication
  • Get link to a final report
  • Get QC report
  • Get user details
  • Get user details with authentication
  • Get VCF files
  • Get whole genome view PNG
  • Get workflow names
  • Start an analysis
  • Query by sample name API call
  • Unshare analyses
  • View=summary
• Programming guidelines for Ion Reporter Software plugins
  • Guidelines to develop Ion Reporter Software plugins
• Oncomine Variant Annotator plugin criteria
  • Oncomine BRCA Research Assay
  • Oncomine Breast cfDNA Assay
  • Oncomine Breast cfDNA Research Assay v2
  • Oncomine Childhood Cancer Research Assay
  • Oncomine Colon cfDNA Assay
  • Oncomine Comprehensive Assay v3
  • Oncomine Comprehensive Assay Plus
  • Oncomine Focus Assay
  • Oncomine Lung Cell‑Free Total Nucleic Acid Research Assay
  • Oncomine Lung cfDNA Assay
  • Oncomine Myeloid Assay
  • Oncomine Myeloid MRD Assays
  • Oncomine Pan‑Cancer Cell‑Free Assay
  • Oncomine tumor specific panels
  • Oncomine Tumor Mutation Load Assay
  • Custom panel assay
  • Ion Torrent Class-Based Variants
• Documentation and support
  • Related documentation
  • Customer and technical support
  • Limited product warranty
• Legal