Set Analysis Parameters
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1.
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Open the Enrichment app from BaseSpace Sequence Hub as follows. |
- Select the Apps tab, and then select Enrichment.
- From the Version drop-down list, select 3.1.0.
- Select Launch Application.
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2.
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To override the default analysis name, enter a preferred analysis name in the Analysis Name field. |
The default is the app name with the date and time the session started.
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3.
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Select Select Project. |
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4.
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In the Select Projects dialog box, select where to store app results, and then select Select. |
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5.
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From the Biosample(s) field, select the biosample you want to analyze as follows. |
- Select Select Biosample(s).
- Select the checkbox of each biosample you want to analyze, and then select Select.
The labels of this field and button in the software interface might be different from the labels in this guide, depending on the BaseSpace Sequence Hub mode. In New mode, all data that is associated with the selected biosample is used in the analysis.
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6.
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From the Sample BAM file(s) field, select Select Dataset File(s), and then browse to the BAM file you want to use. |
Multiple BAM files can be selected.
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7.
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From the Reference Genome drop-down list, select the reference genome. |
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8.
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From the Targeted Regions drop-down list, select one of the following targeted regions: |
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Illumina Exome Panel v1.2 (CEX) |
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IDT xGen Exome Research Panel v1.0 |
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TruSight Inherited Disease v1.0 |
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TruSight One Expanded v2.0 |
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TruSight Hereditary Cancer v2.0 |
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9.
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If you selected Custom Manifest from Targeted Regions, select Select Dataset File(s), and then select a manifest file. |
If the manifest file you want to use is not listed, see Upload a Manifest File for instructions on how to import the manifest.
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10.
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From the Base Padding drop-down list, select the base padding value. |
This setting 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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11.
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For Variant Caller, select from the following options: |
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Germline—Used for most other nontumor sample types. |
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Somatic—Used for tumor samples. |
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12.
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To enable SV calling, select the Enable SV Calling checkbox. |
SV calling is disabled by default.
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13.
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To enable CNV calling, clear the Enable CNV Calling checkbox. |
CNV calling is disabled by default.
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14.
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If you enabled CNV calling, select Select Biosample(s) from the Control Biosample(s) for CNV calling field, and select a control sample file(s) for CNV calling. |
Up to five control samples can be selected.
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15.
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For Annotation, select from the following options. |
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RefSeq—Variants are annotated using RefSeq transcripts. |
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Ensembl—Variants are annotated using Ensembl transcripts. |
Variant annotation is supported for human genomes only, and not supported for custom genomes.
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16.
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[Optional] Select the Set Advanced Options drop-down list to view the advanced options and specify the values for the appropriate options. See Advanced Options. |
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17.
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Select Launch Application to start the analysis. |
When analysis is complete, the app session status is automatically updated and you receive a confirmation email.