# ICA Analysis

### Link Bundles

1. Link the DRAGEN 4.5 bundle in ICA to ICA project.
2. See ICA reference pages for more details on adding bundles: <https://help.ica.illumina.com/home/h-bundles>
3. See ICA reference pages for more details on uploading data: <https://help.ica.illumina.com/project/p-data>

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### Executing DRAGEN Germline Analysis

**WARNING**: Deviation from these instructions (including adding additional options) may cause pipeline failure.

1. Select the DRAGEN\_Germline\_Whole\_Genome\_4-5-2 Pipeline. Select to start analysis with that pipeline.

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2. Enter the necessary run information such as user reference tags, outputs and logs folder.\
   Select the necessary input files for the run, including sample inputs. .FASTQ.GZ or .FASTQ.ORA are supported inputs, optionally with an FASTQ list file. Select "Homo sapiens \[1000 Genomes] hg38 v6 Pangenome" for the reference genome.<br>

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3. By **default**, Map/Align Options, Variant Calling Options, CNV Options, and SV Options **are enabled** for the DRAGEN 4.5.2 version and is recommended. If no Small Variant Calling, CNV or SV Calling is desired, set those options to "False" (screenshot displays the button to click; the box will disappear upon selecting "False" for those settings). \\

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**NOTE**: SV results are turned on to improve CNV calling accuracy, but these results are not verified or supported.

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4. Navigate to the **Illumina TruPath Genome Options** section of the analysis input settings.

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5. By **default**, "Enable Proximity Mode" for use with Illumina TruPath Genome is check-marked and enabled. <mark style="color:red;">**NOTE:**</mark> This option must be enabled in order to analyze TruPath data.

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6. (Optional): To output an additional Hi-C output file for visualization, checkmark the option for "Enable Illumina TruPath Visualization"

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7. (Optional): To turn on Multi-Region Joint Detection (MRJD) Calling, checkmark the option for "Enable running Illumina TruPath MRJD." Please refer to the DRAGEN User Guide for more information on Multi-Region Joint Detection.<br>

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8. Confirm configured settings. Start the analysis upon configuring all analysis settings.

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