Advanced Options
[Optional] Specify the values for the advanced options.
|
Option |
Description |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Somatic variant caller threshold (percentage) |
If Somatic Variant Calling is enabled, enter a value 0–30 to specify the threshold percentage above which somatic variants are called. The default is 5. A low threshold value can result in more false positive variants. |
||||||||||||
|
CNV caller quality threshold |
If CNV Calling is enabled, enter a value 0–50 to specify the quality score threshold level. The default is 4. A low threshold value can result in more false positive variants. |
||||||||||||
|
Trim Adapters |
Select one of the following trim adapter options:
|
||||||||||||
|
Flag PCR Duplicates |
By default, the app flags PCR duplicates and excludes them for variant calling. If you do not want the app to flag PCR duplicates, clear 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. |
||||||||||||
|
Probes Manifest (for use in Picard HsMetrics) |
By default, the app uses the specified Targeted Regions manifest to generate Picard HS metrics. If you want to use a custom manifest instead, select Use Custom Probes Manifest. |
||||||||||||
|
Custom Probes Manifest |
If you selected the custom targeted manifest and use custom probes manifest options, select the 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. |