Review analysis results for Ion AmpliSeq™ HD panels

  1. In the Analyses tab, click Overview.

    The Analyses table lists all of the available analyses results.

  2. Click the column headings to sort the results. Alternatively, use the available filters or the Search function to limit the list of analyses.
  3. In the Analysis column, click the link to open an analysis of interest.
  4. (Optional) In the Filter Options section, select a filter chain from the Filter Chains list to view analyses results as described.

    If you download filtered variants, the downloaded files reflect the filter chain that is applied and saved to the analysis. Ensure that you click Save Filter Chain to save an applied filter chain to the analysis before you download filtered variants.

    Option

    Description

    Called Variants and Controls

    Default filter chain for the Ion AmpliSeq™ HD analysis workflows. Use this filter chain for analysis results that report all variants (either hotspots or novel) that pass the filter and are not called as reference or NOCALL. Variant types include: SNV, INDEL, MNV, CNV, LONGDEL, FUSION, EXPR_CONTROL_ASSAYS_5P_3P, RNA_HOTSPOT, GENE_EXPRESSION, RNAExonVariant, ProcControl, and FLT3ITD.

    Called Hotpot Variants and Controls

    Select this filter chain for analysis results that report all hotspot variants that pass the filter and are not called as reference or NOCALL. Filter variant types include: SNP and INDEL.

    Variant Matrix Summary

    Select this filter chain for analysis results that replicate data that is shown for Ion AmpliSeq™ HD analysis results in the Variant Matrix Summary.

    Variant types include: SNV/INDEL, CNV, fusions, and RNAExonVariants.

    Oncomine Variants (5.10 or later)

    Apply the Oncomine Variants (5.10 or later) filter chain to show only the variants that are annotated with the Oncomine™ Variant Annotator plugin. For more information, see Oncomine Variant Annotator plugin criteria.

    The analysis results update immediately to reflect the filtered results.

Example of Analysis Results screen, LOD view, and Filter Options pane