Download all variants in an analysis

  1. In the Analyses tab, click Overview, then select the analysis of interest.
  2. Use one of the following options to download a compressed directory of files that contains data for all variants in the analysis:
    • Select the row for the analysis of interest, then click Actions > Download All Variants .

    • Click the hyperlink for the name of the Analysis to open the Analysis Results page, then click Download > All Variants .

    • Click the hyperlink for the name of the Analysis to open the Analysis Results page, then click Visualize, In the Analysis Visualization click Download > All Variants .
  3. To download the compressed directory from Ion Reporter™ Software:
    1. Open the Home tab, then click Notifications.
    2. Find the download file in the list. You can click Downloads to narrow the list, or see the timestamp.
    3. Click (Download).
  4. Extract the contents of the directory to access the folders and files.

    Folder

    Description of contents

    CNV_VCIB

    • cn_results.png, a file that represents the CNV amplicons in the X scale and log2 ratio in Y scale. Open the file with a text editor.

    • amplicon_data.txt

    QC

    • report.pdf

    • Torrent Suite™ Software Quality Control (QC files. For example, bam_file_basename>.ionstats_alignment.json, analysis.bfmask.stats, explog_final.txt, raw_peak_signal, InitLog.txt, basecaller_results/BaseCaller.json, basecaller_results/ datasets_basecaller.json, basecaller_results/ionstats_tf.json, basecaller_results/TFStats.json

    • mapd.txt

    • diffCoverage.seg

    • RNAQCAndCalls.txt

    • TotalMappedFusionPanelReads.txt

    • qc_cnv_display.txt

    • <analysis name>_QC.pdf

    StatsActor

      • amplicons_low_no_coverage_statistics.txt

      • analysis_low_no_coverage_statistics.txt

      • genes_low_no_coverage_statistics.txt

    • AnnotatorActor

      • variome-stats.csv

    Variants

    Contains VCF and TSV files for the CNV variants. You can open these files in Microsoft™ Excel™.

    Note: If the Ion Reporter™ Software analysis includes notes, the notes are included in the files in a row named #analysisnotes.

    • <analysis name><timestamp>.oncomine.tsv

    • <analysis name><timestamp>.vcf

    • <analysis name><timestamp>.full.tsv

    • SmallVariants.filtered.vcf

    • SmallVariants.vcf

    • Variant.filtered.genome.vcf

    Workflow_Settings

    • Analysis_Settings —Contains a text file that describes settings used for the analysis. Open the file with a text editor.

    • Module_Configuration_Files—Contains configuration files for workflows, including VariantCallerActor.json, a JSON file that contains variant finding parameters used to customize variant calling in Ion Reporter™ Software and the settings used in the analysis. The file shows changes made to the parameters in the software. The file is present only for analyses that contain variants.

    fusions_RNAExonVariants_normCounts.png

    MSI

    Files with data about microsatellite instability (MSI) markers. These markers can identify a form of genomic instability in the replication of repetitive DNA. MSI often occurs in tumor cells. It leads to the appearance of multiple alleles at microsatellite loci, which can be easily identified.

    • Summary.tsv—Provides a summary of results for MSI markers, as shown in the Analysis Results table, and additional information about the algorithm version that is used to calculate the Marker MSI Score and MSI Score.

    • Details.tsv—Provides marker-level information on microsatellite instability, such as individual marker MSI scores, and read coverage for individual MSI markers.

    RESULTS

    If the Tumor Mutational Burden parameter is enabled, or an analysis workflow for the Tumor Mutation Load Assay is used, a Results folder is generated that contains:

    • filter_variants.tsv and somatic_variants.tsv—TSV files that contain post-filter and somatic variants.

    • <tmb report>.pdf—PDF report that contains tumor mutational load results.

    • statistic.txt—contains tumor mutational burden statistics.

    • PNG files that contain images of:

      • allele frequency distribution of germline and somatic variants

      • allele frequency distribution of only somatic variants

      • bar plot of signature type and context of somatic mutations

      • pie chart of substitution type of somatic mutations

      • pie chart of signature pattern of somatic mutations

    Plugin outputs

    Contains ZIP file of the plugin output directory.

    Immune Repertoire Output

    The CSV, PNG and PDF files that show the data for Immune Repertoire analyses.

    • <analysis name><timestamp>.csv

    • <analysis name><timestamp>.png

    • <analysis name><timestamp>.pdf

    Metagenomics Output

    Files that contains reads for the analyses in FASTA format, and other TXT files for the analysis.

    gene_Modules

You can view the extracted files individually, or upload a VCF file to a software that requires VCF files, such as Oncomine™ Reporter Software.