Visualize variants in an analysis run with an Ion AmpliSeq™ HD analysis workflow
You can view a summary of data about the identified variants, and toggle to other views that provide more details about the same variants.
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In the Analyses tab, click Overview.
The Analyses table lists all the available analyses results.
- Click the column headings to sort the results. Alternatively, use the available filters or the Search field to limit the list of analyses.
- Select the checkbox in the row of the analysis that you want to visualize or select two or more analyses if you want to visualize a side-by-side comparison of multiple results.
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Click Visualize.
The Analysis Visualization screen opens to the Variant Matrix tab, displaying the Summary screen that shows all the identified SNVs/INDELs, CNVs, and Fusions.
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Review detailed variant data.
In the Variant Matrix tab, in the Summary screen, click the gene name in the Gene column to access the HGNC report for that gene.
(Fusion analyses only) In the RNA Exon Variant tab, visualize normalized counts within gene for each exon variant.
Click SNV/INDEL, CNV, or Fusion to view detailed analysis metrics. For a description of each metric, see Detailed analysis metrics.
In the SNV/INDEL, CNV, or Fusion screen, click the link in the Locus column to view specific variants in the Ion Reporter™ Genomic Viewer (IRGV) in a separate window.
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Review proband read coverage tracks.
Ion AmpliSeq™ HD analyses group consensus reads into families. A family is a group of reads that are associated with the same DNA molecule before library amplification. Each family is identified using the molecular tags, and consensus reads with the same molecular tags are grouped into the same family. In IRGV data view, the color of the consensus reads is used to indicate a family. Side by side consensus reads with the same color belong to the same family.
Within each read track, each nucleotide variant is indicated by a different color. T, A, C, and G are red, green, blue, and orange, respectively. An "I" denotes insertion, and white color with a dash indicates deletion.
You can sort, adjust, and view details about variants and base calls that are visualized in each read coverage track.
Note: The number of molecules in the (IRGV) coverage track can be slightly different from what is reported in the VCF output. The values seen in IRGV are based on initial estimates made by the variant caller, whereas read or molecular counts in VCF output are based on calculations that can include additional processing by the variant detection pipeline.
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Generate Visualization Report.
- In the IRGV & Generate Report tab, click Generate Report.
- In the Select Visualization Report Template, select an existing template from the dropdown list or select Create New Report Template, then click OK.
- If needed, modify the report configuration, then proceed to the Preview step.
- Click to download the PDF report.