Analyze on Illumina Connected Analytics
Configure a DRAGEN for ILMN Cell-Free DNA Prep with Enrichment pipeline analysis in ICA with the following parameters. The name of the parameter in the software interface may differ, depending on the software platform in use.
For information about using and configuring pipelines, refer to the Illumina Connected Analytics documentation.
Settings and Files
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Analysis Data
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Tumor FASTQs—Tumor data files in FASTQ format. |
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[Optional] Tumor FASTQ list—CSV list of tumor FASTQ files. |
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Reference—Custom reference TAR file. |
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Target BED (Manifest)—The BED file that contains your custom targeted regions. |
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Map Align and UMI
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UMI minimum supporting reads—Minimum number of input reads with matching UMI and position required to generate a consensus read. The default value is 2.
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Map-align output format—File format for map-align output. Possible options are BAM or CRAM.
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Small Variant Calling Settings
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Enable Small variant calling—Enables small variant calling.
If enabled, provides options for small variant analysis.
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Small Variant Caller Output
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VCF and GVCF—Variants are recorded individually and nonvariants are grouped into blocks. |
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VCF and GVCF with BP_RESOLUTION—Variants and nonvariants are recorded individually. This option is typically used for debugging and increases run time and gVCF file size. |
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Somatic variant quality filter threshold—Somatic variants with a quality score less than this threshold level are marked as filtered. The range of this setting is 0–30. The default value is 0.7. |
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Use somatic hotspots for small variant calling—Options for using somatic hotspots. |
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True—Use predefined regions matched to the selected reference. |
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False—Omit predefined regions or use regions listed in an attached custom somatic hotspots file. |
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Base padding—The base padding to add to each target BED region.
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This option is used to pad targeted regions for variant calling and does not affect most enrichment metrics.
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Variant annotation—Option to enable or disable variant annotation. |
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Variant annotation asssembly—Assembly to use for variant annotation. |
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Small Variant Calling Files
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Baseline systematic noise BED—Systematic noise BED file.Systematic noise detection is automatically enabled when a noise BED file is specified. |
You can use the BaseSpace Sequence Hub CNV Baseline Builder app to create baseline files.
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Excluded regions file—BED file that defines regions to exclude. |
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Custom somatic hotspots file—VCF file that defines the custom list of somatic hotspots.
To enable custom hotspots, set Use somatic hotspots for small variant calling as false. |
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Custom TMB CH variant regions file—BED file that defines custom regions for TMB calculation. |
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CNV Settings and FIles
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Enable CNV calling—Enables copy number variant calling. If enabled, uses the following files:
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CNV Baseline Files/Panel of Normals—CNV baseline files.
Files must be of the same type (eg, all .target.counts or files or all .target.counts.gc-corrected. |
You can use the BaseSpace Sequence Hub CNV Baseline Builder app to create baseline files.
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[Optional] Custom CNV BED File—BED file that indicates the target intervals to use for sample coverage.
If a custom file is not specified, analysis uses the default enrichment regions. |
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[Optional] CNV combined counts—Combined panel of normals file.
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Structural Variants
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Enables structural variant analysis.
Enable SV calling—Enables structural variant calling.
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Locus node regions BED—BED file (in *.bed or *.bed.gz format) for targeted calling of locus node target regions. SV caller settings are modified for increased sensitivity within this region.
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Additional Options
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Additional DRAGEN args—DRAGEN command-line arguments. Refer to the DRAGEN Bio-IT Platform documentation for more information. |
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Samples per node—The number of sample inputs processed per node.
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Error strategy—Pipeline options for failed samples.
The following options are supported: |
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Terminate—Terminate analysis.
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Ignore—Proceed with analysis. Sample errors are recorded in log files.
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