Set Analysis Parameters
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Navigate to the BaseSpace Sequence Hub, and then click the Apps tab. |
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In the Search Apps field, enter the app name, and then select the app icon. |
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Select version 3.0.0 from the drop-down list, and then click Launch to open the app. |
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At the Analysis Name field, enter the analysis name. |
By default, the analysis name includes the app name, followed by the date and time
that the analysis session starts.
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At the Save Results To field, select the project that stores the app results. |
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At the Samples field, browse to the sample or BAM files you want to analyze and select the checkbox. |
You can analyze up to 96 samples per analysis.
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At the Reference Genome field, select the reference genome. |
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At the Targeted Regions field, select 1 of the following targeted regions: |
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Nextera Rapid Capture Exome v1.2 (default) |
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Nextera Rapid Capture Expanded Exome v1.0 |
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TruSeq Expanded Exome v1.0 |
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TruSeq Rapid Exome v1.2 |
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TruSeq Rapid Expanded Exome v1.0 |
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TruSight Cardiomyopathy v1.0 |
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TruSight Inherited Disease v1.0 |
NOTE
If you select Custom Manifest as the targeted region, select the targeted manifest file. In Advanced Options, select the probes manifest file. If you do not want to use probes manifest, deselect the Generate Picard HS Metrics and Per Target Coverage Information checkbox.
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At the Base Padding field, select the base padding. |
The default is 150. Base padding defines the amount of sequence immediately upstream and downstream of the targeted regions that is used to calculate padded enrichment statistics.
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At the Small Variant Caller field, select the germline (Starling) or somatic (Pisces) variant calling option. |
In the Advanced Options, you can change the somatic variant caller threshold when you select somatic variant calling.
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Select the Enable SV Calling checkbox for structural variant calling (Manta). |
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Select the Enable CNV Calling checkbox for copy number variant calling (Canvas), and then select the control samples for CNV calling. |
The CNV control samples must be different from the input samples.
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From the Annotation field, select the gene and transcript annotation reference database to use. |
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[Optional] Select the Set Advanced Options drop-down arrow to view the advanced options. |
Specify the values for the appropriate options. See Advanced Options.
The Enrichment App begins analysis.
When analysis is complete, the app updates the status of the session and sends an email to notify you.
Enrichment v3.0 Online Help
For Research Use Only. Not for use in diagnostic procedures.