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