Compare multiple analyses and download a TSV file

You can compare multiple analyses, filter the variants that appear in the visualizations of the compared analyses, and download the collective results of the multiple analyses in a TSV file. Comparisons can be used to analyze results and identify common or unique hotspots of interest across analyses. TSV files that contain the results of multiple analyses can be downloaded separately or in a batch download that also includes VCF result files for each analysis. To download a TSV file from the IRGV & Generate Report tab, RNA Exon Variant tab, or TMB tab, you need to download the TSV file in a folder of files. For more information, see Variants file downloads.

When you compare analysis results from one, 2, or 3 similar analyses, the software generates a Venn diagram to show the sets of variants that are common between the analysis results. The sets of variants that are not common between the selected analyses. You can use the Venn diagram to select the unique or common sets of variants to narrow and refine the list of variants that are displayed in the Variant Table.

Venn diagrams are generated in Ion Reporter™ Software for 2 or 3 sets of analysis results. For more information, see Venn diagram generation. Venn diagrams are not generated for Ion AmpliSeq™ HD, Tagseq, immune repertoire, metagenomics, and microbiome analysis workflows, although you can make comparisons across similar analysis results with these analysis workflows.

In the Analysis tab, click Overview, then select multiple analyses.

Note: You can use the filters above the Analyses table to view only analyses of interest. For more information, see Find analyses.
Click ActionsVisualize in the Selected Analyses section.
The Analysis Visualization screen opens to the TMB tab.
Click the Variants Table tab.
The table view shows side-by-side columns that list the variants for the analyses.
Refine the list of variants in the Filter Options section:
1. Click the number in the overlapping set of the Venn diagram or other set of interest.
2. Click Filter to update the table to include only the selected variants.
3. (Optional) Click Clear to deselect all variants and restore the list to include all variants.
  
  Note: You can place the pointer over a sample name in the Venn diagram to see the full sample name and the analysis to which the sample belongs. The analysis name is listed in parentheses.
(Optional) View the filtered results in other visualization screens. For example, click CNV Heat Map to view a visual representation of copy number variation for the refined variant list.
To download the refined multianalysis results in a TSV file:
1. Click DownloadCurrent Results TSV.
2. Click the Home tab, then click Notifications.
3. Find the download file in the list, then click (Download).
The TSV file that contains the refined list of variants is downloaded. The TSV file is a tab-separated list of the variants. It contains the data and columns presented in the same order shown in the Variants Table.
(Optional) Click Clear to deselect all variants and restore the Variants Table to include all variants.

Note: Under rare circumstances, the TSV file results can be duplicated in the Variants Table results in the Amino acid and Coding columns. This happens when the variant is Ref in one analysis, and a NOCALL in the other analysis.

Clustering in CNV heat map For CNV heat maps, ploidy is used as the score for every gene-sample pair to generate the heat map. After that hierarchical clustering is conducted for clustering genes and samples in the heat map.

Venn diagram generation

Ion Reporter™ Software generates Venn diagrams to display the number of variants that are unique and common between analyses. You can use Venn diagrams to limit visualizations to subsets of variants. For more information, see Samples Venn diagram in Filter Options.

Venn diagrams are generated for up to three similar analyses. Venn diagram generation in the software is analysis workflow, research application, and sample group dependent.

Venn diagrams are generated with following single analysis visualizations.

One DNA Paired analysis.
One DNA Trio analysis.

Venn diagrams are generated with multi-analysis visualizations of any of the analyses combinations.

One DNA Single analysis and one DNA Tumor–Normal analysis.
One DNA Single analysis and one DNA and Fusions analysis.
One DNA Single analysis and one DNA Paired analysis.
One DNA and Fusions analysis and one Fusions analysis.
One DNA Tumor–Normal analysis and one DNA Paired analysis.
Two DNA Single analyses.
Two DNA and Fusions analyses.
Two DNA Tumor–Normal analyses.
Two Fusions analyses.
Two Annotate Variants analyses.

Venn diagrams are generated with multi-analysis visualizations of any of the analyses combinations.

One DNA Single analysis and two DNA Tumor–Normal analyses.
One DNA Tumor–Normal analysis and two DNA Single analyses.
Three DNA Single analyses.
Three DNA and Fusions analyses.
Three DNA Tumor–Normal analyses.
Three Fusions analyses.
Three Annotate Variants analyses.

Venn diagrams are not generated for Ion AmpliSeq™ HD, TagSeq, immune repertoire, metagenomics, and microbiome analysis workflows,