Variants file downloads

You can download a compressed directory of files from a successful analysis that includes variants results in a VCF file. You can use the files to analyze Ion Reporter™ Software data in downstream software, such as Oncomine™ Reporter, or examine VCF files directly. Each downloaded directory also includes files with other analysis results information for variants that are not contained in the VCF file.

You cannot download a variants file for analyses that do not include a VCF file in the results package. For example, analysis results that are launched from the Immune Repertoire or 16 S Metagenomics analysis workflows do not include variants. If a plugin is run, it must generate a VCF file for this procedure to apply.

The contents of each type of variants directories available for download in Ion Reporter™ Software are as follows:

  • Filtered variants—A VCF file and other files, all of which contains variants, or information for the variants, which were filtered IN for the analysis. Variants that are in the VCF file are results that are filtered IN by either the filter chain that is used by default in the analysis workflow, or the filter chain that is saved to the analysis workflow. See Filters and filter chains for more information.

  • All variants—A VCF that contains all variants that are included in the analysis, and other files that contain information for the variants. Variants in this file include those that are called, uncalled and controls.

  • Selected variants—A VCF that contains selected variants from the analysis, and other files that contain information for the variants. Each variant to be included in the selected variants VCF file must be selected in the Analysis Results before the files are downloaded. Variants in this file include those that are called, uncalled and controls.

Downloads of results files can be automated with the web services API that is included with Ion Reporter™ Software. For more information, see Ion Reporter Software web services API.