Local Run Manager Amplicon Analysis Module Workflow Guide (1000000002708 v00)

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