Download selected variants

You can download a VCF file that contains variants that you select, and other files that contain information for the selected variants. Use this option to download files that focus on the variants that are relevant to your research.
  1. In the Analyses tab, click Overview, then select the analysis that contains the filtered variants.
  2. Use one of the following options to download a compressed directory of files that contains data for variants that are filtered:

      1. Click the hyperlink for the name of the Analysis to open the Analysis Results screen.

      2. Select each checkbox for one or more variants of interest to download.

      3. Click Download > Selected Variants.

      1. Click Visualize.
      2. Click Download > Selected Variants.

    A compressed directory that is named analysis name_SelectedVariants.zip is downloaded.

  3. To download the ZIP file 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

    CnvActor

    Gene_deletions.xls, a file that contains information about whole gene deletions and amplicon coverage that are found in BRCA analyses. Values in the third column of the file indicate the following information for the BRCA1 and BRCA2 genes in the sample.

    • S—Stable.

    • SQCFAIL—Calculated overall variation between amplicon coverage is too high.

    • LGD=<score>—Large Gene Deletion with Phred scale score = <score>.

    • WGD=<score>—Whole Gene Deletion with Phred scale score = <score> (max score = 100).

    The Phred scale score is must >=40, for the WGD (subtype = GeneCNV) to be reported in the VCF file. Large gene deletions are not reported in the VCF file.

    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—output of the copy number variation.

    • diffCoverage.seg—output of CNV module.

    • RNAQCAndCalls.txt—contains information on the QC for fusion data.

    • TotalMappedFusionPanelReads.txt—provides number of total mapped fusion panel reads.

    • qc_cnv_display.txt—CNV sample QC for BRCA analyses.

    • <analysis name>_QC.pdf—Report of QC metrics in PDF format. The same QC metrics are available in the Final Report of an analysis.

    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

    • base_change_file.txt and somatic_mutation_substitution_context_summary.txt— four files that contain the data used to generate the substitution type and context of somatic mutations and substitution type and signature pattern of somatic mutations plots

    • deamination_metric.txt — contains the TMB score and other TMB metrics

    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 from a single metagenomics sample, or results from multiple samples that the software compares for Beta diversity, and files that contains reads for the analysis in FASTA format, and other TXT files for the analysis.

    To download all results files for metagenomics analyses, use instead the Download results files for all samples link, shown in the Visualization/Downloads section of the metagenomics analysis results. For more information, see View interactive taxonomy charts for metagenomics analyses.

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

Related Topics
Parent topic: Variants file downloads