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Select settings that are appropriate to both your sequencing instrument and your experiment: Germ-Line – Low Stringency Optimized for high frequency variants and minimal false negative calls. Germ-Line – High Stringency Optimized for high frequency variants and minimal false positive calls.
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Select settings that are appropriate to both your sequencing instrument and your experiment: Germ-Line – Low Stringency Optimized for high frequency variants and minimal false negative calls.

Germ-Line – High Stringency Optimized for high frequency variants and minimal false positive calls. Somatic – Low Stringency Optimized for low frequency variant detection with minimal false negative calls. Somatic – High Stringency Optimized for low frequency variant detection with minimal false positive calls.

Ion Proton data only Custom Settings that you customize. You cannot select this radio button. This button is enabled if you change a parameter value. Your radio button selection loads the correct set of default parameters for that type of run. If you want to customize parameters further, change parameter values in the main settings area. Advanced users can also click the Show Advanced Settings button to change values in the advanced settings.

These notes apply to the Variant Caller Parameter Settings and advanced settings selections: If you do customize settings in the advanced settings area, your changes are overwritten if you select a different Variant Caller Parameter Settings radio button or again click on the same radio button.

If you make changes in the advanced settings and later want to reset these parameters to their default values, again click your Variant Caller Parameter Settings radio button selection. In general, you can safely customize parameters for SNP calling. For indel calling, changes to the parameters tend to have a significant effect in the number of indels called. With indels, the tradeoff between sensitivity and specificity becomes too large. Parameters are categorized as main settings, which are intended for general use, and advanced settings, which allow additional customization of the variant calling algorithm but are intended for advanced users only.

To download the parameters used in a completed TVC run, see Parameters File in Buttons for downloads and other actions. Upload your custom parameter values Use the Upload Custom Settings Choose File button to upload your set of custom parameter settings: You can use this mechanism for the following: To quickly apply your own settings to all your TVC plugin runs To know that your parameters are consistent for instance, that a parameter change is not inadvertently forgotten in the UI To apply a file of settings shared by others The parameters file must be in JSON format.

After upload, the UI reflects the parameter values from your uploaded file. You can still make additional changes in the UI.

Follow these steps to upload a parameters file for your TVC plugin run: Have the JSON file to be uploaded on your local machine. You can optionally edit values in the file before uploading.

Browse to your parameters file and click OK. The optimized parameters are imported into your run and are reflected in the parameter table on the launch page. Input files This section describes input files that you provide for the TVC plugin. Both a target regions file and a hotspots file must be associated with a reference before you use them with the TVC plugin.

You upload these files to a specific reference, such as hg19, in the admin References page. Target regions file A target regions file controls the sequencing and downstream analysis of a targeted resequencing run in this way: In contrast, a whole genome analysis sequences every position that corresponds to the reference genome.

Hotspots file A hotspots file contains a list of positions on the genome and when configured in a workflow affects the analysis results. For each position during variant calling: Evidence for a variant is examined at that position without regard to the hotspots positions and a call is made.

Then the hotspots positions are examined. At each position listed in the file, if a variant is not already called, then one of the following variant calls is added: By default the variantCaller plugin calls variant candidates at hotspot positions with more sensitivity than candidates at other positions. You can customize certain variantCaller parameters separately for hotspot candidates. Icon The Torrent Variant Caller takes a significant amount of time to complete.

Setting it up to run automatically saves time compared to running it manually. See also Variant Caller parameters. Please note, that this functionality is only available via manual launch of TVC after the run and not available from the run planning stage. Select a completed run that you would like to reanalyze with TVC.

Select variantCaller. The Torrent Variant Caller 5. The Configuration tab allows you to Edit, Delete or Add a configuration. The Setup tab allows you to apply settings to individual barcodes.

When finished making changes, click Submit. The TVC plugin reruns and applies the changes you made. Click the Add button to add new. Name the configuration and select your settings. On the Edit screen, you can modify Chip and Library types, variant frequency, reference genome, targeted and hotspots regions and parameter settings.

At the bottom of the screen, you can click the Show Advanced Settings button and further adjust variant detection and alignment parameters. Save your new or modified configurations and then apply them to all or select barcodes. Click Submit to rerun TVC.

Configure the Torrent Variant Caller in a template or run plan Use the run plan template wizard to have the TVC plugin run automatically after the Torrent Suite analysis completes.

Before following these steps, read the Introduction , Supported panels , Parameter Settings defaults , and Variant Caller parameters sections for information about the options and customizations for the plugin. The TVC plugin run uses the same target regions file and hotspots file as the main Torrent Suite Software analysis if those files are present in the main analysis.

Through the wizard there is no facility in the TVC configuration to change the target regions file or hotspots file. You can use a different target regions file and hotspots file with a manual TVC launch from a completed run report.

When you select the plugin chevron in the template or run plan wizard and enable the variantCaller checkbox, a Configuration link appears next to the variantCaller listing: Link the Configure link to open the variantCaller configuration popup: Make your changes to the parameter values.

Advanced users can also click the Show Advanced Settings button and customize those parameters. Be sure to click the Save Changes button before leaving this page. Be sure to click the Save Plugin Settings button before you click Close. Your changes are lost if you do no use the Save Changes button. You can later return to the Variant Caller configuration page by clicking the Configure button next to variantCaller in the Plugin chevron. Changes to parameters can dramatically affect the behavior and sensitivity of the Variant Caller.

Parameter changes are not recommended if you are new to the Variant Caller plugin. Icon The Variant Caller parameter settings are saved in templates but are not saved in run plans. Parameter changes that you make in a run plan affect only that specific run. When you change Variant Caller parameter settings in a template, your changes affect all users who create run plans from that template.

Combine Alignment creates a new run report in the same project. Y ou can open the new combined run report and use the Select plugins to run button to launch the TVC plugin.

To run the Torrent Variant Caller plugin manually, perform the following steps: In the list of plugins, click on variantCaller. The Torrent Variant Caller Plugin interface appears: When you are satisfied with your selections, click Submit.

Your variant caller analysis is queued for execution. Torrent Variant Caller plugin output The Torrent Variant Caller plugin output includes the following reports and sections: Run report plugin summary The run report contains a short summary of plugin output.

These summaries appear below the run report metrics and above the Output Files section. To jump to the plugin results: Click the Plugin Summary jump near the top of the run report: Click the link to go to the TVC results summary: The browser jumps to the variantCaller summary.

The variantCaller summary area is slightly different for barcoded and non-barcoded runs. In both cases, the summary section includes the following: Information about the analysis type, targeted regions and hotspot files, and variantCaller parameter settings.

The total number of variants called. The variantCaller. Download links: The zipped VCF file of variant calls. The results in a tab-separated file. The genome VCF file.

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Discover and download paid and free VST plugins, AU plugins, AAX audio plugins, mastering plugins, equalizer plugins, compressor plugins. Algorithm borrowed from mjeftf.me and adapted to work with zsh. #. function magnet_to_torrent() {. [[ “$1” =~ xt=urn:btih:([^\&/]+) ]] || return . Torrent Suite Software space on Ion Community The Plugin Summary section lists the plugins associated with the analysis, and provides an interface for.

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