Set Analysis Parameters
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1
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Open Whole Genome Sequencing from BaseSpace Sequence Hub as follows. |
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a
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Select the Apps tab, and then select Whole Genome Sequencing. |
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b
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From the Version drop-down list, select 7.0.0. |
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c
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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 was started.
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3
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Select Select Project(s). |
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4
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Select a project to store app results to, and then select Select. |
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5
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Select the biosample you want to analyze as follows. |
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a
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Select Select Biosample(s). |
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b
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Select the checkbox of each biosample you want to analyze, and then select a prep kit you want to use with the biosample. |
You can select multiple samples and prep kits.
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6
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From the Select Sample Bam file(s) field, select the BAM files to use for the analysis. |
You can select multiple BAM files.
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7
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From the Reference Genome drop-down list, select the reference genome you want to reference. |
The default reference genome is Human (NCBI GRCh38 PAR-masked with decoys hs38d1).
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8
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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, copy number variants (CNVs), ExpansionHunter, ROHcaller, and HLATyping.
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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, with coverage over 10x, all checkboxes are selected and the app performs variant, structural variant, and copy number variant calling. With coverage under 10x, variant calling is forced to be off.
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9
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For Annotation, select from the following options 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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Both
—Variants are annotated using both Ensembl and RefSeq transcripts.
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None
—Variants are not annotated.
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10
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Select Continue to start the analysis. |
When the analysis is complete, the status of the app session is automatically updated and you receive a confirmation email.
Whole Genome Sequencing v7.0 App Online Help
For Research Use Only. Not for use in diagnostic procedures.