Analyze on BaseSpace Sequence Hub

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Analysis name—Name of the analysis.

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Project—Project to store analysis results in.

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Biosamples—The biosamples to analyze.

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Reference type—Reference genome source. Enables input options for the selected reference type.

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Target BED manifest file—BED file that contains targeted regions.

Additional Analysis Settings

Category	Setting Description
Small Variant Calling	Small variant calling—Enables small variant calling. If enabled, provides options for small variant analysis. • Small Variant Caller Output • VCF • VCF and GVCF—Variants are recorded individually and nonvariants are grouped into blocks. • 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. • 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. • Base padding—The base padding to add to each target BED region. This option is used to pad targeted regions for variant calling and does not affect most enrichment metrics. • 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. • Excluded regions file—BED file that defines regions to exclude. • Somatic hotspots—List of positions where risk of somatic mutations is expected to be elevated. • None—Do not use hotspot regions. • Built-in—Use predefined regions matched to the selected reference. • Custom—Use a custom list of hotspot regions. • Custom somatic hotspots file—VCF file that defines the custom list of somatic hotspots. Required when the somatic hotspot source is configured to use custom regions. • Custom TMB CH variant regions file—BED file that defines custom regions for TMB calculation. • Variant annotation—Option to enable or disable variant annotation. • Variant annotation asssembly—Assembly to use for variant annotation.
CNV	Enable CNV calling—Enables copy number variant calling. If selected, enables additional options. • 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. • [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.
Structural Variants	Enables structural variant analysis and DNA fusion filter calling. Enable SV calling—Enables structural variant calling. • 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. DNA Fusion Filter—Enables DNA Fusion Filter Calling, which might reduce false positives. • Reference genome—The reference genome to use for fusion filtering.
UMI Settings	• 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. • Map-align output format—File format for map-align output. Possible options are BAM or CRAM.
Advanced Settings	• Samples per node—The number of sample inputs processed per node. • Error strategy—Pipeline options for failed samples. The following options are supported: • Terminate—Terminate analysis. • Ignore—Proceed with analysis. Sample errors are recorded in log files.