Ion Reporter™ Software 5.22 Help

Introduction to Ion Reporter™ Software

About Ion Reporter™ Software

Ion AmpliSeq™ and Ion AmpliSeq™ HD panel types

hg19 and GRCh38 human genome references

Network and password security requirements

Get started with Ion Reporter™ Software

Purchasing and ecommerce

Ion Reporter™ Software on Connect

Ion Reporter™ Server

Ion Reporter™ Software dashboard

View notifications

Status alert emails

Sign-in troubleshooting and support contacts for Ion Reporter™ Software

Set default number of rows displayed in tables

IonReporterUploader command-line utility

Import and manage samples

Samples tab overview

Sample attributes overview

Sample import options

Sample definition

Customize the Samples table

Transfer samples to users in other organizations

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

View analysis workflow details

Predefined analysis workflows

User-defined analysis workflows

Customize tuning parameters

Steps in analysis workflow creation

Workflow presets

Analysis workflow revision autonumbering

Lock an analysis workflow

Analyses tab overview

Customize the Analyses table

Launch an analysis

Launch analyses by batch

Add an analysis note

Delete an analysis

Copy analyses to storage on Connect

Monitor analyses

Reanalyze aborted analysis results

Share data from an analysis

Download BAM files

Download analysis files

Download detailed analysis logs

Analysis results

Analysis Results table overview

Open and review analysis results

Customize the Analysis Results table

Edit Analysis Results

Variants file downloads

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

Microbiome health research analysis results

MSI analysis results

View tumor mutational burden analysis results

View Oncomine™ Myeloid Research Assay analysis results

View metagenomics analysis results

View analysis results for a single sample

Detailed analysis metrics

Visualize analysis results with Ion Reporter™ Software

Genomic segmentation analysis results

Visualize HRR analysis results

Mutational Signature profiles

Time series visualizations

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

Visualize the BRCA report

Adjust IRGV BAM tracks

Sort read coverage tracks by variant

CNV segment data in chromosome view

Visualize an analysis workflow that contains a CNV baseline

Visualize tumor mutational burden analysis results

Compare results of single or multiple analyses

Compare multiple analyses and download a TSV file

Coverage histogram

Evaluate analysis results

Novel fusion detection using expression imbalance

Visualize RNA exon variants

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

Visualize variants with IGV

Visualization interpretation guidance

Create and view reports

Visualization reports

Amplicon coverage reports

Quality Control (QC) reports

Available report sections

Filters and filter chains

About filters and filter chains

View filter chain details

Create a user-defined filter chain

Create a gene symbol filter

Edit a filter chain

Lock a user-defined filter chain in workflow presets

Delete a user-defined filter chain in workflow presets

Filter chain examples

Predefined filter chains

Predefined filters

Annotation sources

Annotations available in Ion Reporter™ Software

Import a custom annotation source

Delete custom annotation sources

Change amino acid code

Variant identifiers for Oncomine™ panels

Preferred transcripts in default analysis workflows

Annotation sources and scores

Annotation versions and calculations

Codon differences in chromosome M

Effect of Ensembl and RefSeq sources on Polyphen and SIFT scores

Genetic Category Type variants

HGVS genomic codes

Ion Reporter™ Software references

PolyPhen-2 score

Administer Ion Reporter™ Software

Admin tab overview

Manage system services

View software version information

Manage archives

Manage policies

Manage audit records

Reset the API token for Ion Reporter™ Software on Connect

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

Data types for gene fusions analyses

Fusion sample QC metrics

Fusion detection methods

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

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 user details

Get user details with authentication

Get whole genome view PNG

Get analysis workflow names

Start an analysis

Query by sample name API call

Unshare analyses

View a list of analyses

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 Research Assays

Oncomine™ Myeloid MRD (RUO) Assays

Oncomine™ Pan‑Cancer Cell‑Free Assay

Oncomine™ tumor specific panels

Oncomine™ Tumor Mutation Load Assay

Ion Torrent™ class-based variants

Documentation and support

Related documentation

Customer and technical support

Limited product warranty

aligned read length

alpha-beta diversity

amplicon coverage

annotation-only analysis workflow

annotation set preset

annotation source

average base coverage depth

average base read depth

barcode crosstalk

basecalling input file

base substitution classes

cellularity (%)

CNV baseline preset

control sequence

copy number gain

copy number loss

coverage histogram

de novo assembly

FD (flow disruptiveness)

filter chain preset

final report template preset

frameshift insertion or deletion

functional score

genomic coordinates

GRCh38 human reference

non-frameshift insertion or deletion

no template control

primer dimer ISP

reference library

relationship group

structural variants

target regions file

test fragment ISPs

tumor mutational burden

tumor-normal pair

unaligned reads

Ion Reporter™ Software web services API

Important Licensing Information