Set Analysis Parameters
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1
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Navigate to BaseSpace, and then click the Apps tab. |
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3
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From the drop-down list, select version 2.1.0, and then click Launch to open the app. |
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4
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In 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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5
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From the Save Results To field, select the project that stores the app results. |
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6
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From the Sample(s) [96 maximum] field, browse to the sample you want to analyze, and select the checkbox. |
You can select multiple samples, with a maximum of 96 samples in 1 session.
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7
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From the Reference Genome field, select the reference genome you want to align. |
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8
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From the Targeted Regions field, select the targeted region of your enrichment. |
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9
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From the Custom Targeted Manifest field, select the custom targeted manifest file for analysis. |
This option is available if you selected Custom Manifest from the Targeted Regions field drop-down list.
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10
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From the Aligner field, select the aligner. The default is BWA-MEM. |
BWA-MEM is optimized for alignment of modern Illumina sequencing data. BWA-backtrack can be used for consistency with legacy data.
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11
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From the Base Padding field, select the padding. The default is 150. |
Padding defines the amount of sequence immediately upstream and downstream of the targeted regions that is also used in enrichment analysis.
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12
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From the Annotation field, select the gene and transcript annotation reference database. The default is RefSeq. |
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13
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Optional, click the Advance drop-down list for additional parameter fields. |
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a
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From the Trim Adapters field, select the adapters to trim. Use this setting if adapter trimming has not already been applied as a sample sheet setting. |
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b
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From the Flag PCR Duplicates field, select the checkbox if you want the app to flag PCR duplicates in the BAM files and to not used for variant calling. PCR duplicates are defined as two clusters from a paired-end run where both clusters have the exact same alignment positions for each read. Optical duplicates are already filtered out during RTA processing. PCR duplicates are not applicable for single-end samples. |
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c
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From the Generate Picard HS Metrics and Per Target Coverage Information field, select the checkbox to generate Picard HS metrics. See Picard Metrics for more information. |
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d
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From the Custom Probes Manifest field, select the custom probes manifest file for analysis. This field is required when you select the Custom Targeted Manifest and Generate Picard HS Metrics and per target coverage information options. |
The BWA Enrichment App begins the analysis of the sample.
When analysis is complete, the app updates the status of the session and an email is sent to notify you.
BWA Enrichment v2.1 App Online Help