Set Analysis Parameters
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1
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Open the app from BaseSpace Sequence Hub as follows. |
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b
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Click Whole Genome Sequencing. |
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c
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From the drop-down list, select version 5.0.0, and then click Launch. |
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2
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[Optional] In the Analysis Name field, enter an analysis name of your preference. |
The default is the app name followed by the date and time the analysis session started.
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3
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Click Select Project(s). |
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4
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In the Save Project(s) dialog box, click a project to store the app results, and then click Select. |
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5
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Click Select Sample(s). |
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6
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In the Select Sample(s) dialog box, select the checkbox of each sample to include in the analysis, and then click Select. |
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7
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Select either FASTQ files or BAM files. |
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In the Select Sample FASTQ Files field, browse to the FASTQ files you want to analyze and select the checkbox. |
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In the Select Sample BAM Files field, browse to the BAM files you want to analyze and select the checkbox. |
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8
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Click the Reference Genome drop-down arrow, and then select the reference genome. |
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9
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[Optional] Clear any of the following checkboxes to disable specific types of variant calling: |
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Enable Variant Calling
—Clearing this checkbox disables calling of structural variants (SVs), single nucleotide variants (SNVs), Indels, and copy number variants (CNVs).
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Enable SV Calling
—Clearing this checkbox disables SV calling only.
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Enable CNV Calling
—Clearing this checkbox disables CNV calling only.
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By default, all checkboxes are selected and the app performs variant, structural variant, and copy number variant calling.
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10
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Click an Annotation option to specify the variant annotation database to use. |
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Ensembl
—Variants are annotated using Ensembl transcripts.
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RefSeq
—Variants are annotated using RefSeq transcripts.
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None
—Variants are not annotated.
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11
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[Optional] Expand the Advanced area to view additional parameters. |
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Clear the Flag PCR Duplicates checkbox to use PCR duplicates for variant calling. |
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12
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Click Continue to start the analysis. |
When analysis is complete, the app session status is automatically updated and you are notified via email.
Whole Genome Sequencing v5.0 App Online Help
For Research Use Only. Not for use in diagnostic procedures.