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Advanced Options
[Optional] Specify the values for the advanced options.
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Option |
Description |
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Somatic variant caller threshold percentage |
Enter the threshold percentage above which somatic variants are called. The default is 5. A low threshold value can result in more false positive variants. |
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Trim Adapters |
Select 1 of the following trim adapter options:
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Flag PCR Duplicates |
By default, the app flags PCR duplicates and not use them for variant calling. If you do not want the app to flag PCR duplicates, deselect the checkbox. PCR duplicates are 2 clusters that have the exact same alignment positions for each read and are from a paired-end run. This option is available for paired-end data sets. |
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Generate Picard HS Metrics and Per Target Coverage Information |
By default, the app generates the Picard HS metrics. If you do not want the app to generate the metrics, deselect the checkbox. |
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Custom Probes Manifest |
When you select the custom targeted manifest option and the generate Picard HS metrics and per target coverage information option, you are required to upload the manifest file. |
For Research Use Only. Not for use in diagnostic procedures.