Custom Analysis Settings
Custom analysis settings are intended for technically advanced users. If settings are applied incorrectly, serious problems can occur.
Add a Custom Analysis Setting
1 From the Module-Specific Settings section of the Create Run screen, click Show
advanced module settings.
2 Click Add custom setting.
3 In the custom setting field, enter the setting name as listed in the Available Analysis
Settings section.
4 In the setting value field, enter the setting value.
5 To remove a setting, click the x icon.
Available Analysis Settings
}
Variant Frequency—Filters variants with a frequency less than the specified threshold. If using the Somatic Variant Caller, adjust the value for this setting on the
Create Run screen.
Setting Name
VariantFrequencyFilterCutoff
Setting Value
Enter a threshold value.
With the Somatic Variant Caller, the default value is 0.05.
With GATK or Starling, the default value is 0.20.
}
Indel Repeat Cutoff—Filters insertions and deletions when the reference has a 1base or 2-base motif over 8 times (by default) next to the variant. If using the Somatic
Variant Caller, enable or disable this setting on the Create Run screen.
Setting Name
IndelRepeatFilterCutoff
Setting Value
Enter a threshold value.
The default value is 8.
} Variant Genotyping Quality—Filters variants with a genotype quality (GQ) less than the specified threshold.
Setting Name
VariantMinimumGQCutoff
Setting Value
Enter a value less than 99.
With GATK or Somatic Variant Caller, the default value is 30.
With Starling, the default value is 20.
} Variant Quality Cutoff—Filters variants with a quality (QUAL) less than the specified threshold. QUAL indicates the confidence of the variant call.
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Setting Name
VariantMiniumQualCutoff
Setting Value
Enter a threshold value.
With GATK or Somatic Variant Caller, the default value is 30.
With Starling, the default value is 20.
Local Run Manager Amplicon Analysis Module Workflow Guide
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Notes