# NovaSeq X Settings

## Standalone Sections

### Header Section

<table data-full-width="false"><thead><tr><th width="208">Parameter</th><th width="107">Required</th><th>Description</th><th>Requirements</th></tr></thead><tbody><tr><td>Custom_*</td><td>No</td><td>Custom field used to capture run metadata.</td><td>String with ASCII characters except for * and the control characters CR and LF.</td></tr><tr><td>FileFormatVersion</td><td>Yes</td><td>Used to identify the sample sheet as a v2 sample sheet. This field must always exist in the header section with a value of 2.</td><td>Must always be 2.</td></tr><tr><td>InstrumentPlatform</td><td>No</td><td><p>Identifies the instrument platform to be used for the run.</p><p>For example, enter <code>NovaSeqXSeries</code> for NovaSeq X Series.</p></td><td>String with ASCII characters except for * and the control characters CR and LF.</td></tr><tr><td>InstrumentType</td><td>No</td><td><p>Identifies the instrument to be used for the run.</p><p>For example: if using NovaSeq X, populate the field with NovaSeq X.</p></td><td>String with ASCII characters except for * and the control characters CR and LF.</td></tr><tr><td>RunDescription</td><td>No</td><td>The run description can contain 255 alphanumeric characters, spaces, dashes, and underscores.</td><td>String with ASCII characters except for * and the control characters CR and LF.</td></tr><tr><td>RunName</td><td>Yes</td><td>The run name can contain 255 alphanumeric characters, spaces, dashes, and underscores.</td><td>String with ASCII characters except for * and the control characters CR and LF.</td></tr></tbody></table>

### Reads Sections

<table data-full-width="false"><thead><tr><th width="171">Parameter</th><th width="97">Required</th><th width="153">Description</th><th>Requirements</th></tr></thead><tbody><tr><td>Index1Cycles</td><td>No¹</td><td>Number of cycles in Index Read 1. Required if more than one sample is present in sample sheet.</td><td><ul><li>Must be an integer ≥ 0.</li><li>Depending on your sequencing system and reagent kit, there can be limitations on the number of cycles in the Index Read.</li><li>Warning if values in range [1–5] inclusive.</li><li>If there is more than 1 sample per lane, must be > 0.</li><li>If OverrideCycles is present in the BCL_Settings section, must be consistent with the sum of the Index1 section of OverrideCycles.</li></ul></td></tr><tr><td>Index2Cycles</td><td>No¹</td><td>Number of cycles in Index Read 2. Required if using dual indexes for demultiplexing.</td><td><ul><li>Must be an integer ≥ 0.</li><li>Depending on your sequencing system and reagent kit, there can be limitations on the number of cycles in the Index Read.</li><li>Warning if values in range [1–5] inclusive.</li><li>If OverrideCycles is present in the BCL_Settings section, must be consistent with the sum of the Index1 section of OverrideCycles.</li></ul></td></tr><tr><td>Read1Cycles</td><td>Yes</td><td>Number of cycles for Read 1.</td><td><ul><li>Must be an integer > 0.</li><li>Warning if less than 26.</li><li>If OverrideCycles is present in the BCL_Settings section, must be consistent with the sum of the Read1 section of OverrideCycles.</li></ul></td></tr><tr><td>Read2Cycles</td><td>Yes</td><td>Number of cycles for Read 2. Required only when running a paired-end sequencing run.</td><td><ul><li>Must be an integer ≥ 0.</li><li>Warning if values in range [1–25] inclusive.</li><li>If OverrideCycles is present in the BCL_Settings section, must be consistent with the sum of the Read2 section of OverrideCycles.</li></ul></td></tr></tbody></table>

¹ Depending on the run or library prep kit, this parameter might be required.

### Sequencing Section

<table data-full-width="false"><thead><tr><th width="235">Parameter</th><th width="102">Required</th><th>Description</th><th>Requirements</th></tr></thead><tbody><tr><td>CustomIndex1Primer</td><td>No¹</td><td>Indicates if a Custom Index 1 primer is used for the run.</td><td>Values <code>true</code> and <code>false</code> allowed. Value true only allowed if <code>Index1Cycles</code> is specified.</td></tr><tr><td>CustomIndex2Primer</td><td>No¹</td><td>Indicates if a Custom Index 2 primer is used for the run.</td><td>Values <code>true</code> and <code>false</code> allowed. Value true only allowed if <code>Index2Cycles</code> is specified.</td></tr><tr><td>CustomRead1Primer</td><td>No¹</td><td>Indicates if a Custom Read 1 primer is used for the run.</td><td>Values <code>true</code> and <code>false</code> allowed. Value true only allowed if <code>Read1Cycles</code> is specified.</td></tr><tr><td>CustomRead2Primer</td><td>No¹</td><td>Indicates if a Custom Read 2 primer is used for the run.</td><td>Values <code>true</code> and <code>false</code> allowed. Value true only allowed if <code>Read2Cycles</code> is specified.</td></tr><tr><td>LibraryPrepKits</td><td>Yes</td><td>Identifies the library prep kit used for the run.</td><td><ul><li>String with ASCII characters except for * and the control characters <code>CR</code> and <code>LF</code>.</li><li>If more than one library prep kit is being used, use semicolons to separate the names of the different library prep kits.</li></ul></td></tr></tbody></table>

¹ Depending on the run or library prep kit, this parameter might be required.

## Application Sections

For NovaSeq X Series, there is a limit of four application sections for onboard analysis or eight application sections for cloud analysis.

### BCL Convert

{% tabs %}
{% tab title="4.3.13" %}
**BCLConvert\_Settings**

<table><thead><tr><th width="242">Parameter</th><th width="103">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the software to be used to perform BCL conversion on the Sample_ID's that only exist in the BCL Convert Data section of the sample sheet. The version is specified using all three integers included in the DRAGEN version name. For example, 1.0.0.</td></tr><tr><td>FastqCompressionFormat</td><td>Yes</td><td>The compression format for the FASTQ output files.<br>Allowed values are gzip or dragen.</td></tr><tr><td>GenerateFastqcMetrics</td><td>No</td><td>Enable/disable generation of FAST QC Metrics. Default = False. If included in the Sample Sheet, then all DRAGEN versions (for BCL Convert and non-BCL Convert workflows) must be 4.3.13 or later. Not applicable for the Cloud pipeline mode.</td></tr><tr><td>CreateFastqForIndexReads</td><td>No</td><td>See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>TrimUMI</td><td>No</td><td>See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>AdapterBehavior</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>AdapterStringency</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MinimumTrimmedReadLength</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MinimumAdapterOverlap</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MaskShortReads</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>NoLaneSplitting</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>FindAdaptersWithIndels</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>IndependentIndexCollisionCheck</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr></tbody></table>

**BCLConvert\_Data**

<table><thead><tr><th width="250">Parameter</th><th width="102">Required</th><th>Description</th></tr></thead><tbody><tr><td>AdapterRead1</td><td>No</td><td><p>The sequence of the Read 1 adapter to be<br>masked or trimmed. To trim multiple adapters,<br>separate the sequences with a plus sign (+)<br>indicating independent adapters that must be<br>independently assessed for masking or<br>trimming for each read. Characters must be A,<br>C, G, or T.</p><p>A value of na (case insensitive) must be used if:</p><ul><li>the AdapterRead1 field is placed in the Data section of the Sample Sheet, and</li><li>no adapter trimming is desired for the sample</li></ul></td></tr><tr><td>AdapterRead2</td><td>No</td><td>See description of AdapterRead1, applied to AdapterRead2.</td></tr><tr><td>BarcodeMismatchesIndex1</td><td>No</td><td><p>Specifies barcode mismatch tolerance for Index 1. Possible values are 0, 1, or 2, or na.<br>The default value is 1. Only allowed if Index is specified in RunInfo.xml file and in the Reads section of the Sample Sheet.</p><p>A value of na must be used if:</p><ul><li>BarcodeMismatchesIndex1 exists in the Data section of the Sample Sheet, and</li><li>OverrideCycles exist in the data section, and</li><li>Index 1 is masked out for the sample in the OverrideCycles</li></ul></td></tr><tr><td>BarcodeMismatchesIndex2</td><td>No</td><td>See description of BarcodeMismatchesIndex1, applied to BarcodeMismatchesIndex2.</td></tr><tr><td>OverrideCycles</td><td>No</td><td><p>Specifies the sequencing and indexing cycles to be used when processing the sequencing data. Must adhere to the Specifies the sequencing and indexing cycles to be used when processing the sequencing data. Must adhere to the following requirements:<br>• Must be same number of fields (delimited by semicolon) as sequencing and indexing reads specified in RunInfo.xml and in the Reads section of the Sample Sheet.<br>• Indexing reads are specified with I, sequencing reads are specified with Y, UMI cycles are specified with U, and trimmed<br>reads are specified with N.<br>• The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file and in the Reads section of the Sample Sheet.<br>• Only one Y or I sequence can be specified per read.</p><ul><li>'I' cycles can only be specified for index reads</li><li>'Y' cycles can only be specified for genomic reads</li><li><p>The total number of cycles used for demultiplexing each index cannot exceed 27. Note that this includes all cycles between the first "I" cycle used by any sample and the last "I" cycle used by any sample within each index.</p><ul><li>"I5N3;I5N3" : counts as 5 bases toward the limit of 27 for Index1, and as 5 bases toward the limit of 27 for Index2</li><li>"I4N1I3;I5N3": counts as 8 bases toward the limit of 27 for Index1, and as 5 bases toward the limit of 27 for Index2</li></ul></li></ul><p>The following are examples of OverrideCycles input:<br>U8Y143;I8;I8;U8Y143<br>N10Y66;I6;N10Y66<br></p><p>For a sample sheet containing two samples having the following OverrideCycles:</p><ul><li>Y151; I8N2; N10; Y151</li><li>Y151; N2I8; I8N2; Y151</li></ul><p>the number of cycles used for demultiplexing sums to 18.</p><p>For sequencers with RunInfo.xml having "IsReverseComplement" set to "Y" for Index2, then Index2 is processed in reverse complement orientation. Any trimming should be applied to the end of the sequence as it transitions to the adapter, which means the "N" cycles specified in OverrideCycles must be in the beginning of the index read.</p><p>Example of 8bp i5 index with the last two (adapter) bases to be trimmed:</p><ul><li>Forward i5: XXATCGCGGT</li><li>ReverseComp i5: ACCGCGATXX (this is the direction of sequencing)</li><li>OverrideCycles for Index2: N2I8</li></ul><p>where XX is part of the adapter sequence.</p><p>Although Index2 is processed on the sequencer in reverse complement format, Index2 and OverrideCycles are entered in the Sample Sheet in forward, non-complemented format for user convenience (see diagram below).</p><p>Note that NovaSeq X has a RunInfo.xml with "IsReverseComplement" set to "Y" for Index2.</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td><p>ID for the sample with the following requirements:<br>• Must be alphanumeric string with _ or - and no<br>spaces.<br>• Case sensitive (i.e., a Sample Sheet with the samples MySample and mysample is not allowed)</p><ul><li>The same Sample_ID may exist on more than one row of the Sample Sheet (e.g., one sample spanning more than one lane)</li><li>Undetermined is not allowed as a Sample_ID</li></ul></td></tr><tr><td>Lane</td><td>Yes</td><td><p>Specifies FASTQ files only for the samples with the<br>specified lane number.</p><p>Must adhere to the following requirements:</p><ul><li>Must be an integer</li><li>Value must be in the range of lanes specified in RunInfo.xml</li><li>Ranges are not supported with '-' or '+'</li><li>If not supplied, it is assumed that all samples are present in all lanes specified in the RunInfo.xml</li><li>If supplied, only lanes specified in the column will be converted from BCL to FASTQ</li></ul><p>For NovaSeqX, values must be in the range of lanes specified in RunInfo.xml</p><ul><li><p></p><ul><li>1.5B Flow Cell: 1-2</li><li>10B Flow Cell: 1-8</li><li>25B Flow Cell: 1-8</li></ul></li></ul></td></tr><tr><td>Index</td><td>Yes</td><td><p>The Index 1 (i7) index sequence. Format is a<br>sequence using ACTG. Required if index cycles are specified for the sample in the OverrideCycles.</p><p>Must adhere to the following requirements:</p><ul><li>Can only contain A, C, G, or T</li><li>Length of string must match number of first index cycles in RunInfo.xml or the number specified in OverrideCycles</li></ul><p>A value of NA must be used if:</p><ul><li>No indexes are specified in OverrideCycles for a sample</li></ul></td></tr><tr><td>Index2</td><td>No</td><td>See description of Index, applied to Index2.</td></tr><tr><td>Sample_Project</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a>. "Logs" and "Reports" are invalid values.</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.23" %}
**BCLConvert\_Settings**

<table><thead><tr><th width="245">Parameter</th><th width="111">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the software to be used to perform BCL conversion on the Sample_ID's that only exist in the BCL Convert Data section of the sample sheet., The version is specified using all three integers included in the DRAGEN version name. For example, 1.0.0.</td></tr><tr><td>FastqCompressionFormat</td><td>Yes</td><td>The compression format for the FASTQ output files.<br>Allowed values are gzip or dragen.</td></tr></tbody></table>

**BCLConvert\_Data**

<table><thead><tr><th width="245">Parameter</th><th width="114">Required</th><th>Description</th></tr></thead><tbody><tr><td>AdapterRead1</td><td>No</td><td><p>The sequence of the Read 1 adapter to be<br>masked or trimmed. To trim multiple adapters,<br>separate the sequences with a plus sign (+)<br>indicating independent adapters that must be<br>independently assessed for masking or<br>trimming for each read. Characters must be A,<br>C, G, or T.</p><p>A value of na (case insensitive) must be used if:</p><ul><li>the AdapterRead1 field is placed in the Data section of the Sample Sheet, and</li><li>no adapter trimming is desired for the sample</li></ul></td></tr><tr><td>AdapterRead2</td><td>No</td><td>See description of AdapterRead1, applied to AdapterRead2.</td></tr><tr><td>BarcodeMismatchesIndex1</td><td>No</td><td><p>Specifies barcode mismatch tolerance for Index 1. Possible values are 0, 1, or 2, or na.<br>The default value is 1. Only allowed if Index is specified in RunInfo.xml file and in the Reads section of the Sample Sheet.</p><p>A value of na must be used if:</p><ul><li>BarcodeMismatchesIndex1 exists in the Data section of the Sample Sheet, and</li><li>OverrideCycles exist in the data section, and</li><li>Index 1 is masked out for the sample in the OverrideCycles</li></ul></td></tr><tr><td>BarcodeMismatchesIndex2</td><td>No</td><td>See description of BarcodeMismatchesIndex1, applied to BarcodeMismatchesIndex2.</td></tr><tr><td>OverrideCycles</td><td>No</td><td><p>Specifies the sequencing and indexing cycles to be used when processing the sequencing data. Must adhere to the following requirements:<br>• Must be same number of fields (delimited by<br>semicolon) as sequencing and indexing reads specified in RunInfo.xml <del>or</del> and in the Reads section of the Sample Sheet.<br>• Indexing reads are specified with I, sequencing reads are specified with Y, UMI cycles are specified with U, and trimmed<br>reads are specified with N.<br>• The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file and in the Reads section of the Sample Sheet.<br>• Only one Y or I sequence can be specified per read.</p><ul><li>'I' cycles can only be specified for index reads</li><li>'Y' cycles can only be specified for genomic reads</li><li><p>The total number of cycles used for demultiplexing by both indexes together cannot exceed 27. Note that this includes all cycles between the first "I" cycle used by any sample and the last "I" cycle used by any sample within each index.</p><ul><li>"I5N3;I5N3" : counts as 10 bases toward the limit of 27</li><li>"I4N1I3;I5N3": counts as (8+5) 13 bases toward the limit of 27</li></ul></li></ul><p>The following are examples of OverrideCycles<br>input:<br>U8Y143;I8;I8;U8Y143<br>N10Y66;I6;N10Y66</p><p>For a sample sheet containing two samples having the following OverrideCycles</p><ul><li>Y151; I8N2; N10; Y151</li><li>Y151; N2I8; I8N2; Y151</li></ul><p>the number of cycles used for demultiplexing sums to 18.</p><p>For sequencers with RunInfo.xml having "IsReverseComplement" set to "Y" for Index2, then Index2 is processed in reverse complement orientation. Any trimming should be applied to the end of the sequence as it transitions to the adapter, which means the "N" cycles specified in OverrideCycles must be in the beginning of the index read.</p><p>Example of 8bp i5 index with the last two (adapter) bases to be trimmed:</p><ul><li>Forward i5: XXATCGCGGT</li><li>ReverseComp i5: ACCGCGATXX (this is the direction of sequencing)</li><li>OverrideCycles for Index2: N2I8</li></ul><p>where XX is part of the adapter sequence.</p><p>Although Index2 is processed on the sequencer in reverse complement format, Index2 and OverrideCycles are entered in the Sample Sheet in forward, non-complemented format for user convenience (see diagram below).</p><p>Note that NovaSeq X has a RunInfo.xml with "IsReverseComplement" set to "Y" for Index2.</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td><p>ID for the sample with the following requirements:<br>• Must be alphanumeric string with _ or - and no<br>spaces.<br>• Case sensitive (i.e., a Sample Sheet with the samples MySample and mysample is not allowed)</p><ul><li>The same Sample_ID may exist on more than one row of the Sample Sheet (e.g., one sample spanning more than one lane)</li><li>Undetermined is not allowed as a Sample_ID</li></ul></td></tr><tr><td>Lane</td><td>Yes</td><td><p>Specifies FASTQ files only for the samples with the<br>specified lane number.</p><p>Must adhere to the following requirements:</p><ul><li>Must be an integer</li><li>Value must be in the range of lanes specified in RunInfo.xml</li><li>Ranges are not supported with '-' or '+'</li><li>If not supplied, it is assumed that all samples are present in all lanes specified in the RunInfo.xml</li><li>If supplied, only lanes specified in the column will be converted from BCL to FASTQ</li></ul><p>For NovaSeqX, values must be in the range of lanes specified in RunInfo.xml</p><ul><li><p></p><ul><li>1.5B Flow Cell: 1-2</li><li>10B Flow Cell: 1-8</li><li>25B Flow Cell: 1-8</li></ul></li></ul></td></tr><tr><td>Index</td><td>Yes</td><td><p>The Index 1 (i7) index sequence. Format is a<br>sequence using ACTG. Required if index cycles are specified for the sample in the OverrideCycles.</p><p>Must adhere to the following requirements:</p><ul><li>Can only contain A, C, G, or T</li><li>Length of string must match number of first index cycles in RunInfo.xml or the number specified in OverrideCycles</li></ul><p>A value of na must be used if:</p><ul><li>No indexes are specified in OverrideCycles for a sample</li></ul></td></tr><tr><td>Index2</td><td>No</td><td>See description of Index, applied to Index2.</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.7" %}
**BCLConvert\_Settings**

<table><thead><tr><th>Parameter</th><th width="105">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the software to be used to perform BCL conversion on the Sample_ID's that only exist in the BCL Convert Data section of the sample sheet., The version is specified using all three integers included in the DRAGEN version name. For example, 1.0.0.</td></tr><tr><td>FastqCompressionFormat</td><td>Yes</td><td>The compression format for the FASTQ output files.<br>Allowed values are gzip or dragen.</td></tr></tbody></table>

**BCLConvert\_Data**

<table><thead><tr><th width="197">Parameter</th><th width="122">Required</th><th>Description</th></tr></thead><tbody><tr><td>AdapterRead1</td><td>No</td><td><p>The sequence of the Read 1 adapter to be<br>masked or trimmed. To trim multiple adapters,<br>separate the sequences with a plus sign (+)<br>indicating independent adapters that must be<br>independently assessed for masking or<br>trimming for each read. Characters must be A,<br>C, G, or T.</p><p>A value of na (case insensitive) must be used if:</p><ul><li>the AdapterRead1 field is placed in the Data section of the Sample Sheet, and</li><li>no adapter trimming is desired for the sample</li></ul></td></tr><tr><td>AdapterRead2</td><td>No</td><td>See description of AdapterRead1, applied to AdapterRead2.</td></tr><tr><td>BarcodeMismatchesIndex1</td><td>No</td><td><p>Specifies barcode mismatch tolerance for Index 1. Possible values are 0, 1, or 2, or na.<br>The default value is 1. Only allowed if Index is specified in RunInfo.xml file and in the Reads section of the Sample Sheet.</p><p>A value of na must be used if:</p><ul><li>BarcodeMismatchesIndex1 exists in the Data section of the Sample Sheet, and</li><li>OverrideCycles exist in the data section, and</li><li>Index 1 is masked out for the sample in the OverrideCycles</li></ul></td></tr><tr><td>BarcodeMismatchesIndex2</td><td>No</td><td>See description of BarcodeMismatchesIndex1, applied to BarcodeMismatchesIndex2.</td></tr><tr><td>OverrideCycles</td><td>No</td><td><p>Specifies the sequencing and indexing cycles to be used when processing the sequencing data. Must adhere to the following requirements:<br>• Must be same number of fields (delimited by<br>semicolon) as sequencing and indexing reads specified in RunInfo.xml <del>or</del> and in the Reads section of the Sample Sheet.<br>• Indexing reads are specified with I, sequencing reads are specified with Y, UMI cycles are specified with U, and trimmed<br>reads are specified with N.<br>• The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file and in the Reads section of the Sample Sheet.<br>• Only one Y or I sequence can be specified per read.</p><ul><li>'I' cycles can only be specified for index reads</li><li>'Y' cycles can only be specified for genomic reads</li><li><p>The total number of cycles used for demultiplexing by both indexes together cannot exceed 27. Note that this includes all cycles between the first "I" cycle used by any sample and the last "I" cycle used by any sample within each index.</p><ul><li>"I5N3;I5N3" : counts as 10 bases toward the limit of 27</li><li>"I4N1I3;I5N3": counts as (8+5) 13 bases toward the limit of 27</li></ul></li></ul><p>The following are examples of OverrideCycles<br>input:<br>U8Y143;I8;I8;U8Y143<br>N10Y66;I6;N10Y66</p><p>For a sample sheet containing two samples having the following OverrideCycles</p><ul><li>Y151; I8N2; N10; Y151</li><li>Y151; N2I8; I8N2; Y151</li></ul><p>the number of cycles used for demultiplexing sums to 18.</p><p>For sequencers with RunInfo.xml having "IsReverseComplement" set to "Y" for Index2, then Index2 is processed in reverse complement orientation. Any trimming should be applied to the end of the sequence as it transitions to the adapter, which means the "N" cycles specified in OverrideCycles must be in the beginning of the index read.</p><p>Example of 8bp i5 index with the last two (adapter) bases to be trimmed:</p><ul><li>Forward i5: XXATCGCGGT</li><li>ReverseComp i5: ACCGCGATXX (this is the direction of sequencing)</li><li>OverrideCycles for Index2: N2I8</li></ul><p>where XX is part of the adapter sequence.</p><p>Although Index2 is processed on the sequencer in reverse complement format, Index2 and OverrideCycles are entered in the Sample Sheet in forward, non-complemented format for user convenience (see diagram below).</p><p>Note that NovaSeq X has a RunInfo.xml with "IsReverseComplement" set to "Y" for Index2.</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td><p>ID for the sample with the following requirements:<br>• Must be alphanumeric string with _ or - and no<br>spaces.<br>• Case sensitive (i.e., a Sample Sheet with the samples MySample and mysample is not allowed)</p><ul><li>The same Sample_ID may exist on more than one row of the Sample Sheet (e.g., one sample spanning more than one lane)</li><li>Undetermined is not allowed as a Sample_ID</li></ul></td></tr><tr><td>Lane</td><td>Yes</td><td><p>Specifies FASTQ files only for the samples with the<br>specified lane number.</p><p>Must adhere to the following requirements:</p><ul><li>Must be an integer</li><li>Value must be in the range of lanes specified in RunInfo.xml</li><li>Ranges are not supported with '-' or '+'</li><li>If not supplied, it is assumed that all samples are present in all lanes specified in the RunInfo.xml</li><li>If supplied, only lanes specified in the column will be converted from BCL to FASTQ</li></ul><p>For NovaSeqX, values must be in the range of lanes specified in RunInfo.xml</p><ul><li><p></p><ul><li>1.5B Flow Cell: 1-2</li><li>10B Flow Cell: 1-8</li><li>25B Flow Cell: 1-8</li></ul></li></ul></td></tr><tr><td>Index</td><td>Yes</td><td><p>The Index 1 (i7) index sequence. Format is a<br>sequence using ACTG. Required if index cycles are specified for the sample in the OverrideCycles.</p><p>Must adhere to the following requirements:</p><ul><li>Can only contain A, C, G, or T</li><li>Length of string must match number of first index cycles in RunInfo.xml or the number specified in OverrideCycles</li></ul><p>A value of na must be used if:</p><ul><li>No indexes are specified in OverrideCycles for a sample</li></ul></td></tr><tr><td>Index2</td><td>No</td><td>See description of Index, applied to Index2.</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.5" %}
**BCLConvert\_Settings**

<table><thead><tr><th width="262">Parameter</th><th width="90">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the software to be used to perform BCL conversion on the Sample_ID's that only exist in the BCL Convert Data section of the sample sheet., The version is specified using all three integers included in the DRAGEN version name. For example, 1.0.0.</td></tr><tr><td>FastqCompressionFormat</td><td>Yes</td><td>The compression format for the FASTQ output files.<br>Allowed values are gzip or dragen.</td></tr><tr><td>GenerateFastqcMetrics</td><td>No</td><td>Import option only. Enable/disable generation of FAST QC Metrics. Default = True.</td></tr><tr><td>CreateFastqForIndexReads</td><td>No</td><td>See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>TrimUMI</td><td>No</td><td>See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>AdapterBehavior</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>AdapterStringency</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MinimumTrimmedReadLength</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MinimumAdapterOverlap</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>MaskShortReads</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>NoLaneSplitting</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>FindAdaptersWithIndels</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr><tr><td>IndependentIndexCollisionCheck</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion</a></td></tr></tbody></table>

**BCLConvert\_Data**

<table><thead><tr><th width="228">Parameter</th><th width="103">Required</th><th>Description</th></tr></thead><tbody><tr><td>AdapterRead1</td><td>No</td><td><p>The sequence of the Read 1 adapter to be<br>masked or trimmed. To trim multiple adapters,<br>separate the sequences with a plus sign (+)<br>indicating independent adapters that must be<br>independently assessed for masking or<br>trimming for each read. Characters must be A,<br>C, G, or T.</p><p>A value of na (case insensitive) must be used if:</p><ul><li>the AdapterRead1 field is placed in the Data section of the Sample Sheet, and</li><li>no adapter trimming is desired for the sample</li></ul></td></tr><tr><td>AdapterRead2</td><td>No</td><td>See description of AdapterRead1, applied to AdapterRead2.</td></tr><tr><td>BarcodeMismatchesIndex1</td><td>No</td><td><p>Specifies barcode mismatch tolerance for Index 1. Possible values are 0, 1, or 2, or na.<br>The default value is 1. Only allowed if Index is specified in RunInfo.xml file and in the Reads section of the Sample Sheet.</p><p>A value of na must be used if:</p><ul><li>BarcodeMismatchesIndex1 exists in the Data section of the Sample Sheet, and</li><li>OverrideCycles exist in the data section, and</li><li>Index 1 is masked out for the sample in the OverrideCycles</li></ul></td></tr><tr><td>BarcodeMismatchesIndex2</td><td>No</td><td>See description of BarcodeMismatchesIndex1, applied to BarcodeMismatchesIndex2.</td></tr><tr><td>OverrideCycles</td><td>No</td><td><p>Specifies the sequencing and indexing cycles to be used when processing the sequencing data. Must adhere to the following requirements:<br>• Must be same number of fields (delimited by<br>semicolon) as sequencing and indexing reads specified in RunInfo.xml and in the Reads section of the Sample Sheet.<br>• Indexing reads are specified with I, sequencing reads are specified with Y, UMI cycles are specified with U, and trimmed<br>reads are specified with N.<br>• The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file and in the Reads section of the Sample Sheet.<br>• Only one Y or I sequence can be specified per read.</p><ul><li>'I' cycles can only be specified for index reads</li><li>'Y' cycles can only be specified for genomic reads</li><li><p>The total number of cycles used for demultiplexing each index cannot exceed 27. Note that this includes all cycles between the first "I" cycle used by any sample and the last "I" cycle used by any sample within each index.</p><ul><li>"I5N3;I5N3" : counts as 5 bases toward the limit of 27 for Index1, and as 5 bases toward the limit of 27 for Index2</li><li>"I4N1I3;I5N3": counts as 8 bases toward the limit of 27 for Index1, and as 5 bases toward the limit of 27 for Index2</li></ul></li></ul><p>The following are examples of OverrideCycles<br>input:<br>U8Y143;I8;I8;U8Y143<br>N10Y66;I6;N10Y66</p><p>For a sample sheet containing two samples having the following OverrideCycles</p><ul><li>Y151; I8N2; N10; Y151</li><li>Y151; N2I8; I8N2; Y151</li></ul><p>the number of cycles used for demultiplexing sums to 18.</p><p>For sequencers with RunInfo.xml having "IsReverseComplement" set to "Y" for Index2, then Index2 is processed in reverse complement orientation. Any trimming should be applied to the end of the sequence as it transitions to the adapter, which means the "N" cycles specified in OverrideCycles must be in the beginning of the index read.</p><p>Example of 8bp i5 index with the last two (adapter) bases to be trimmed:</p><ul><li>Forward i5: XXATCGCGGT</li><li>ReverseComp i5: ACCGCGATXX (this is the direction of sequencing)</li><li>OverrideCycles for Index2: N2I8</li></ul><p>where XX is part of the adapter sequence.</p><p>Although Index2 is processed on the sequencer in reverse complement format, Index2 and OverrideCycles are entered in the Sample Sheet in forward, non-complemented format for user convenience (see diagram below).</p><p>Note that NovaSeq X has a RunInfo.xml with "IsReverseComplement" set to "Y" for Index2.</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td><p>ID for the sample with the following requirements:<br>• Must be alphanumeric string with _ or - and no<br>spaces.<br>• Case sensitive (i.e., a Sample Sheet with the samples MySample and mysample is not allowed)</p><ul><li>The same Sample_ID may exist on more than one row of the Sample Sheet (e.g., one sample spanning more than one lane)</li><li>Undetermined is not allowed as a Sample_ID</li></ul></td></tr><tr><td>Lane</td><td>Yes</td><td><p>Specifies FASTQ files only for the samples with the<br>specified lane number.</p><p>Must adhere to the following requirements:</p><ul><li>Must be an integer</li><li>Value must be in the range of lanes specified in RunInfo.xml</li><li>Ranges are not supported with '-' or '+'</li><li>If not supplied, it is assumed that all samples are present in all lanes specified in the RunInfo.xml</li><li>If supplied, only lanes specified in the column will be converted from BCL to FASTQ</li></ul><p>For NovaSeqX, values must be in the range of lanes specified in RunInfo.xml</p><ul><li><p></p><ul><li>1.5B Flow Cell: 1-2</li><li>10B Flow Cell: 1-8</li><li>25B Flow Cell: 1-8</li></ul></li></ul></td></tr><tr><td>Index</td><td>Yes</td><td><p>The Index 1 (i7) index sequence. Format is a<br>sequence using ACTG. Required if index cycles are specified for the sample in the OverrideCycles.</p><p>Must adhere to the following requirements:</p><ul><li>Can only contain A, C, G, or T</li><li>Length of string must match number of first index cycles in RunInfo.xml or the number specified in OverrideCycles</li></ul><p>A value of na must be used if:</p><ul><li>No indexes are specified in OverrideCycles for a sample</li></ul></td></tr><tr><td>Index2</td><td>No</td><td>See description of Index, applied to Index2.</td></tr><tr><td>Sample_Project</td><td>No</td><td>Import option only. See <a href="https://help.dragen.illumina.com/product-guides/dragen-v4.3/bcl-conversion">DRAGEN Product Docs</a>.</td></tr></tbody></table>
{% endtab %}
{% endtabs %}

### DRAGEN Germline

{% tabs %}
{% tab title="4.3.13" %}
**DragenGermline\_Settings**

<table><thead><tr><th width="216">Parameter</th><th width="109">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenGermline pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Germline), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenGermline\_Data**

<table><thead><tr><th width="215">Parameter</th><th width="105">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, CNV, Repeat Expansions, ROH, CYP2D6, CYP2B6, CYP21A2, SMN, GBA, LPA, RH, and SMN (silent carrier).</p></td></tr><tr><td>QcCoverage1BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage1BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCoverage2BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage2BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCoverage3BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage3BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCrossContaminationVcfFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no<br>spaces allowed. If QcCrossContaminationVcfFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.23" %}
**DragenGermline\_Settings**

<table><thead><tr><th width="203">Parameter</th><th width="103">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software<del>,</del> used to process the DragenGermline pipeline, including conversion to FASTQ, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Germline), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenGermline\_Data**

<table><thead><tr><th width="224">Parameter</th><th width="107">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, CNV, Repeat Expansions, ROH, CYP2D6, CYP2B6, CYP21A2, SMN, and GBA.</p></td></tr><tr><td>QcCoverage1BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage1BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCoverage2BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage2BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCoverage3BedFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If QcCoverage3BedFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>QcCrossContaminationVcfFile</td><td>No</td><td>File name in text (*.txt) or gzip (*.gz) format. Must include the prefix DragenGermline/. Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no<br>spaces allowed. If QcCrossContaminationVcfFile exists in the Data section, but a file is not provided, a value of na must be specified.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.7" %}
**DragenGermline\_Settings**

<table><thead><tr><th width="222">Parameter</th><th width="101">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software<del>,</del> used to process the DragenGermline pipeline, including conversion to FASTQ, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Germline), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenGermline\_Data**

<table><thead><tr><th width="215">Parameter</th><th width="102">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, CNV, Repeat Expansions, ROH, CYP2D6, CYP2B6, CYP21A2, SMN, and GBA.</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.5" %}
**DragenGermline\_Settings**

<table><thead><tr><th width="225">Parameter</th><th width="104">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software<del>,</del> used to process the DragenGermline pipeline, including conversion to FASTQ, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Germline), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenGermline\_Data**

| Parameter          | Required | Description                                                                                                                                                                                                         |
| ------------------ | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| ReferenceGenomeDir | Yes      | Genome name consisting of alphanumeric string with "\_" or "-" or ".".                                                                                                                                              |
| VariantCallingMode | Yes      | <p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, CNV, Repeat Expansions, ROH, CYP2D6.</p> |
| Sample\_ID         | Yes      | See description in the BCL Convert section                                                                                                                                                                          |
| {% endtab %}       |          |                                                                                                                                                                                                                     |
| {% endtabs %}      |          |                                                                                                                                                                                                                     |

### DRAGEN Enrichment

{% tabs %}
{% tab title="4.3.13" %}
**DragenEnrichment\_Settings**

<table><thead><tr><th width="211">Parameter</th><th width="104">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenEnrichment pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Enrichment), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenEnrichment\_Data**

<table><thead><tr><th width="226">Parameter</th><th width="139">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>Bedfile</td><td>Conditionally required</td><td>BED file to be used for analysis in text (*.txt) or gzip (*.gz) format. Only required if VariantCallingMode is not None. Must include the prefix DragenEnrichment/ before the BED file name. Alphanumeric string with _ or - or . with no spaces allowed. The value must be na if BedFile is placed in the Data section and VariantCallingMode = None.</td></tr><tr><td>GermlineOrSomatic</td><td>Yes</td><td>Accepted values are germline or somatic.</td></tr><tr><td>AuxNoiseBaselineFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxCnvPanelOfNormalsFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPanelOfNormalsFile is placed in the Data section and no AuxCnvPanelOfNormalsFile is provided for the sample.</p></td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>AuxCnvPopBAlleleVcfFile</td><td>No</td><td>Alphanumeric string with _ or - or . with no spaces allowed. Text or gzip format. Optional only if VariantCallingMode = AllVariantCallers and GermlineOrSomatic=somatic. Error otherwise. A note should be added to the UI to indicate that CNV output will only be generated if this file is provided.</td></tr><tr><td>AuxGermlineTaggingFile</td><td>No</td><td>Alphanumeric string with _ or - or . with no spaces allowed. Binary file with .bin extension. Optional when SmallVariantCaller or AllVariantCaller option selected and GermlineOrSomatic=somatic. Error otherwise.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.23" %}
**DragenEnrichment\_Settings**

<table><thead><tr><th width="206">Parameter</th><th width="117">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenEnrichment pipeline, including conversion to FASTQ, , Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Enrichment), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenEnrichment\_Data**

<table><thead><tr><th>Parameter</th><th width="132">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>Bedfile</td><td>Conditionally required</td><td>BED file to be used for analysis in text (*.txt) or gzip (*.gz) format. Only required if VariantCallingMode is not None. Must include the prefix DragenEnrichment/ before the BED file name. Alphanumeric string with _ or - or . with no spaces allowed. The value must be na if BedFile is placed in the Data section and VariantCallingMode = None.</td></tr><tr><td>GermlineOrSomatic</td><td>Yes</td><td>Accepted values are germline or somatic.</td></tr><tr><td>AuxNoiseBaselineFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxCnvPanelOfNormalsFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPanelOfNormalsFile is placed in the Data section and no AuxCnvPanelOfNormalsFile is provided for the sample.</p></td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.7" %}
**DragenEnrichment\_Settings**

<table><thead><tr><th width="203">Parameter</th><th width="98">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenEnrichment pipeline, including conversion to FASTQ, , Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Enrichment), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenEnrichment\_Data**

<table><thead><tr><th width="215">Parameter</th><th width="132">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>Bedfile</td><td>Conditionally required</td><td>BED file to be used for analysis in text (*.txt) or gzip (*.gz) format. Only required if VariantCallingMode is not None. Must include the prefix DragenEnrichment/ before the BED file name. Alphanumeric string with _ or - or . with no spaces allowed. The value must be na if BedFile is placed in the Data section and VariantCallingMode = None.</td></tr><tr><td>GermlineOrSomatic</td><td>Yes</td><td>Accepted values are germline or somatic.</td></tr><tr><td>AuxNoiseBaselineFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxCnvPanelOfNormalsFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPanelOfNormalsFile is placed in the Data section and no AuxCnvPanelOfNormalsFile is provided for the sample.</p></td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.5" %}
**DragenEnrichment\_Settings**

<table><thead><tr><th width="233">Parameter</th><th width="101">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenEnrichment pipeline, including conversion to FASTQ, , Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN Enrichment), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. If MapAlignOutFormat is None, VariantCallingMode cannot be None for any sample</td></tr></tbody></table>

**DragenEnrichment\_Data**

<table><thead><tr><th width="228">Parameter</th><th width="131">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".".</td></tr><tr><td>Bedfile</td><td>Conditionally required</td><td>BED file to be used for analysis in text (*.txt) or gzip (*.gz) format. Only required if VariantCallingMode is not None. Must include the prefix DragenEnrichment/ before the BED file name. Alphanumeric string with _ or - or . with no spaces allowed. The value must be na if BedFile is placed in the Data section and VariantCallingMode = None.</td></tr><tr><td>GermlineOrSomatic</td><td>Yes</td><td>Accepted values are germline or somatic.</td></tr><tr><td>AuxNoiseBaselineFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxCnvPanelOfNormalsFile</td><td>No</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPanelOfNormalsFile is placed in the Data section and no AuxCnvPanelOfNormalsFile is provided for the sample.</p></td></tr><tr><td>VariantCallingMode</td><td>Yes</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}
{% endtabs %}

### DRAGEN RNA

{% tabs %}
{% tab title="4.3.13" %}
**DragenRna\_Settings**

<table><thead><tr><th width="200">Parameter</th><th width="116">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenRna pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN RNA), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. Selecting none is not allowed if RnaPipelineMode is set to FulPipeline for any sample.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>DifferentialExpressionEnable</td><td>No</td><td>Accepted values are true or false. If DifferentialExpressionEnable is true, then RnaPipelineMode must be FullPipeline</td></tr></tbody></table>

**DragenRna\_Data**

<table><thead><tr><th width="230">Parameter</th><th width="119">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>RnaGeneAnnotationFile</td><td>No</td><td>Genotype reference file. Alphanumeric string with "_" or "-" or "." with no spaces allowed. If DifferentialExpressionEnable is True., the GTF file must be provided by the user or included with the reference genome.</td></tr><tr><td>RnaPipelineMode</td><td>Yes</td><td>Accepted values are MapAlign or FullPipeline. The full pipeline option includes quantification and fusion detection.</td></tr><tr><td>DownSampleNumReads</td><td>No</td><td>Specifies the number of fragments to downsample to. For paired-end sequencing, the number of reads at the down-sampling output will be twice the number of fragments specified. Accepted values are integers. If DownSampleNumReads is placed in the Data section, and downsampling is not desired for that sample, a value of na must be used.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr><tr><td>Comparison1</td><td>No</td><td>Accepted values are control, comparison, or na. Use only if DifferentialExpressionEnable is true. If RNAPipelineMode is MapAlign, this value must be na. Must have at least 2 control and 2 comparison samples. May have a max of 15 control or comparison samples. All control and comparison samples must have FullPipeline for RnaPipelineMode value and have the same ReferenceGenomeDir and RnaGeneAnnotationFile values.<br><br><br><br><br></td></tr><tr><td>Comparison2</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison3</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison4</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison5</td><td>No</td><td>See Comparison1 Description.</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.23" %}
**DragenRna\_Settings**

<table><thead><tr><th width="262">Parameter</th><th width="108">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenRna pipeline, including conversion to FASTQ,, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN RNA), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. Selecting none is not allowed if RnaPipelineMode is set to FulPipeline for any sample.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>DifferentialExpressionEnable</td><td>No</td><td>Accepted values are true or false. If DifferentialExpressionEnable is true, then RnaPipelineMode must be FullPipeline</td></tr></tbody></table>

**DragenRna\_Data**

<table><thead><tr><th width="245">Parameter</th><th width="104">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>RnaGeneAnnotationFile</td><td>No</td><td>Genotype reference file. Alphanumeric string with "_" or "-" or "." with no spaces allowed. If DifferentialExpressionEnable is True., the GTF file must be provided by the user or included with the reference genome.</td></tr><tr><td>RnaPipelineMode</td><td>Yes</td><td>Accepted values are MapAlign or FullPipeline. The full pipeline option includes quantification and fusion detection.</td></tr><tr><td>DownSampleNumReads</td><td>No</td><td>Specifies the number of fragments to downsample to. For paired-end sequencing, the number of reads at the down-sampling output will be twice the number of fragments specified. Accepted values are integers. If DownSampleNumReads is placed in the Data section, and downsampling is not desired for that sample, a value of na must be used.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr><tr><td>Comparison1</td><td>No</td><td>Accepted values are control, comparison, or na. Use only if DifferentialExpressionEnable is true. If RNAPipelineMode is MapAlign, this value must be na. Must have at least 2 control and 2 comparison samples. May have a max of 15 control or comparison samples. All control and comparison samples must have FullPipeline for RnaPipelineMode value and have the same ReferenceGenomeDir and RnaGeneAnnotationFile values.<br><br><br><br><br></td></tr><tr><td>Comparison2</td><td>No</td><td>See Comparsion1 description.</td></tr><tr><td>Comparison3</td><td>No</td><td>See Comparsion1 description.</td></tr><tr><td>Comparison4</td><td>No</td><td>See Comparsion1 description.</td></tr><tr><td>Comparison5</td><td>No</td><td>See Comparsion1 description.</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.7" %}
**DragenRna\_Settings**

<table><thead><tr><th width="215">Parameter</th><th width="109">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenRNA pipeline, including conversion to FASTQ,, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN RNA), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. Selecting none is not allowed if RnaPipelineMode is set to FulPipeline for any sample.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>DifferentialExpressionEnable</td><td>No</td><td>Accepted values are true or false. If DifferentialExpressionEnable is true, then RnaPipelineMode must be FullPipeline</td></tr></tbody></table>

**DragenRna\_Data**

<table><thead><tr><th>Parameter</th><th width="105">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>RnaGeneAnnotationFile</td><td>No</td><td>Genotype reference file. Alphanumeric string with "_" or "-" or "." with no spaces allowed. If DifferentialExpressionEnable is True., the GTF file must be provided by the user or included with the reference genome.</td></tr><tr><td>RnaPipelineMode</td><td>Yes</td><td>Accepted values are MapAlign or FullPipeline. The full pipeline option includes quantification and fusion detection.</td></tr><tr><td>DownSampleNumReads</td><td>No</td><td>Specifies the number of fragments to downsample to. For paired-end sequencing, the number of reads at the down-sampling output will be twice the number of fragments specified. Accepted values are integers. If DownSampleNumReads is placed in the Data section, and downsampling is not desired for that sample, a value of na must be used.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr><tr><td>Comparison1</td><td>No</td><td>Accepted values are control, comparison, or na. Use only if DifferentialExpressionEnable is true. If RNAPipelineMode is MapAlign, this value must be na. Must have at least 2 control and 2 comparison samples. May have a max of 15 control or comparison samples. All control and comparison samples must have FullPipeline for RnaPipelineMode value and have the same ReferenceGenomeDir and RnaGeneAnnotationFile values.<br><br><br><br><br></td></tr><tr><td>Comparison2</td><td>No</td><td>See Comparison1 description.</td></tr><tr><td>Comparison3</td><td>No</td><td>See Comparison1 description.</td></tr><tr><td>Comparison4</td><td>No</td><td>See Comparison1 description.</td></tr><tr><td>Comparison5</td><td>No</td><td>See Comparison1 description.</td></tr></tbody></table>

<br>
{% endtab %}

{% tab title="4.1.5" %}
**DragenRna\_Settings**

<table><thead><tr><th width="233">Parameter</th><th width="98">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Yes</td><td>The version of the DRAGEN software used to process the DragenRNA pipeline, including conversion to FASTQ,, Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Yes</td><td>The version of the workflow-specific application (i.e., DRAGEN RNA), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Yes</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output. Selecting none is not allowed if RnaPipelineMode is set to FulPipeline for any sample.</td></tr><tr><td>KeepFastQ</td><td>Yes</td><td>Select whether FASTQs are saved (true)<br>or discarded (false).</td></tr><tr><td>DifferentialExpressionEnable</td><td>No</td><td>Accepted values are true or false. If DifferentialExpressionEnable is true, then RnaPipelineMode must be FullPipeline</td></tr></tbody></table>

**DragenRna\_Data**

<table><thead><tr><th width="246">Parameter</th><th width="102">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Yes</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>RnaGeneAnnotationFile</td><td>No</td><td>Genotype reference file. Alphanumeric string with "_" or "-" or "." with no spaces allowed. If DifferentialExpressionEnable is True., the GTF file must be provided by the user or included with the reference genome.</td></tr><tr><td>RnaPipelineMode</td><td>Yes</td><td>Accepted values are MapAlign or FullPipeline. The full pipeline option includes quantification and fusion detection.</td></tr><tr><td>DownSampleNumReads</td><td>No</td><td>Specifies the number of fragments to downsample to. For paired-end sequencing, the number of reads at the down-sampling output will be twice the number of fragments specified. Accepted values are integers. If DownSampleNumReads is placed in the Data section, and downsampling is not desired for that sample, a value of na must be used.</td></tr><tr><td>Sample_ID</td><td>Yes</td><td>See description in the BCL Convert section</td></tr><tr><td>Comparison1</td><td>No</td><td>Accepted values are control, comparison, or na. Use only if DifferentialExpressionEnable is true. If RNAPipelineMode is MapAlign, this value must be na. Must have at least 2 control and 2 comparison samples. May have a max of 15 control or comparison samples. All control and comparison samples must have FullPipeline for RnaPipelineMode value and have the same ReferenceGenomeDir and RnaGeneAnnotationFile values.<br><br><br><br><br></td></tr><tr><td>Comparison2</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison3</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison4</td><td>No</td><td>See Comparison1 Description.</td></tr><tr><td>Comparison5</td><td>No</td><td>See Comparison1 Description.</td></tr></tbody></table>
{% endtab %}
{% endtabs %}

### DRAGEN Somatic

{% tabs %}
{% tab title="4.3.13" %}
**DragenSomatic\_Settings**

<table><thead><tr><th width="202">Parameter</th><th width="132">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Required</td><td>The version of the DRAGEN software used to process the DragenSomatic pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Required</td><td>The version of the workflow-specific application (i.e., DRAGEN Somatic), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Required</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output.</td></tr><tr><td>KeepFastq</td><td>Required</td><td>Select whether FASTQs are saved (true) or discarded (false).</td></tr></tbody></table>

**DragenSomatic\_Data**

<table><thead><tr><th width="238">Parameter</th><th width="109">Required</th><th>Description</th></tr></thead><tbody><tr><td>AuxNoiseBaselineFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxSvNoiseBaselineFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxSvNoiseBaselineFile is placed in the Data section and no AuxSvNoiseBaselineFile is provided for the sample.</p></td></tr><tr><td>AuxCnvPopBAlleleVcfFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPopBAlleleVcfFile is placed in the Data section and no AuxCnvPopBAlleleVcfFile is provided for the sample. CNV output will only be generated if this file is provided.</p></td></tr><tr><td>AuxGermlineTaggingFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxGermlineTaggingFile is placed in the Data section and no AuxGermlineTaggingFile is provided for the sample. Germline tagging output will only be generated if this file is provided.</p></td></tr><tr><td>VariantCallingMode</td><td>Required</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>Sample_ID</td><td>Required</td><td>See description in the BCL Convert section</td></tr></tbody></table>

\ <br>
{% endtab %}

{% tab title="4.1.23" %}
**DragenSomatic\_Settings**

<table><thead><tr><th width="203">Parameter</th><th width="106">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Required</td><td>The version of the DRAGEN software used to process the DragenSomatic pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Required</td><td>The version of the workflow-specific application (i.e., DRAGEN Somatic), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Required</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output.</td></tr><tr><td>KeepFastq</td><td>Required</td><td>Select whether FASTQs are saved (true) or discarded (false).</td></tr></tbody></table>

**DragenSomatic\_Data**

<table><thead><tr><th width="250">Parameter</th><th width="118">Required</th><th>Description</th></tr></thead><tbody><tr><td>AuxNoiseBaselineFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or ".". and no spaces in text (*.txt) or gzip (*.gz) format. Applicable only if GermlineOrSomatic is Somatic and VariantCallingMode is not None.</p><p>The value must be na if AuxNoiseBaselineFile is placed in the Data section and no AuxNoiseBaselineFile is provided for the sample."</p></td></tr><tr><td>AuxSvNoiseBaselineFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxSvNoiseBaselineFile is placed in the Data section and no AuxSvNoiseBaselineFile is provided for the sample.</p></td></tr><tr><td>AuxCnvPopBAlleleVcfFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxCnvPopBAlleleVcfFile is placed in the Data section and no AuxCnvPopBAlleleVcfFile is provided for the sample. CNV output will only be generated if this file is provided.</p></td></tr><tr><td>AuxGermlineTaggingFile</td><td>Optional</td><td><p>Alphanumeric string with "_" or "-" or "." and no spaces in text (*.txt) or gzip (*.gz) format. Optional if VariantCallingMode is AllVariantCallers.</p><p>The value must be na if AuxGermlineTaggingFile is placed in the Data section and no AuxGermlineTaggingFile is provided for the sample. Germline tagging output will only be generated if this file is provided.</p></td></tr><tr><td>VariantCallingMode</td><td>Required</td><td><p>Variant calling mode for the run.</p><p>Accepted values are None, SmallVariantCaller, AllVariantCallers. The option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided).</p></td></tr><tr><td>Sample_ID</td><td>Required</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}
{% endtabs %}

### DRAGEN Methylation

{% tabs %}
{% tab title="4.3.13" %}
**DragenMethylation\_Settings**

<table><thead><tr><th width="208">Parameter</th><th width="139">Required</th><th>Description</th></tr></thead><tbody><tr><td>SoftwareVersion</td><td>Required</td><td>The version of the DRAGEN software used to process the DragenMethylation pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5.</td></tr><tr><td>AppVersion</td><td>Required</td><td>The version of the workflow-specific application (i.e., DRAGEN Methylation), using all three integers included in the version name. For example, 1.0.0.</td></tr><tr><td>MapAlignOutFormat</td><td>Required</td><td>Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output.</td></tr><tr><td>KeepFastq</td><td>Required</td><td>Select whether FASTQs are saved (true) or discarded (false).</td></tr><tr><td>UsesTaps</td><td>Required</td><td>Select whether the TAPS assay, which directly converts methylated C to T, is used (true) or not used (false)</td></tr></tbody></table>

**DragenMethylation\_Data**

<table><thead><tr><th width="249">Parameter</th><th width="105">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Required</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>MethylationProtocol</td><td>Required</td><td>Select the library protocol for methylation analysis from the set {'directional’, ‘non-directional’, ‘directional-complement’,‘pbat’}</td></tr><tr><td>Sample_ID</td><td>Required</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}

{% tab title="4.1.23" %}
**DragenMethylation\_Settings**

| Parameter         | Required | Description                                                                                                                                                                                                  |
| ----------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| SoftwareVersion   | Required | The version of the DRAGEN software used to process the DragenMethylation pipeline, including conversion to FASTQ. Specified using all three integers included in the DRAGEN version name. For example 4.1.5. |
| AppVersion        | Required | The version of the workflow-specific application (i.e., DRAGEN Methylation), using all three integers included in the version name. For example, 1.0.0.                                                      |
| MapAlignOutFormat | Required | Formatting of the output files. Accepted values are bam, cram, or none. Selecting none produces no map/align output.                                                                                         |
| KeepFastq         | Required | Select whether FASTQs are saved (true) or discarded (false).                                                                                                                                                 |
| UsesTaps          | Required | Select whether the TAPS assay, which directly converts methylated C to T, is used (true) or not used (false)                                                                                                 |

**DragenMethylation\_Data**

<table><thead><tr><th width="233">Parameter</th><th width="123">Required</th><th>Description</th></tr></thead><tbody><tr><td>ReferenceGenomeDir</td><td>Required</td><td>Genome name consisting of alphanumeric string with "_" or "-" or ".". Can be placed in either settings or data section.</td></tr><tr><td>MethylationProtocol</td><td>Required</td><td>Select the library protocol for methylation analysis from the set {'directional’, ‘non-directional’, ‘directional-complement’,‘pbat’}</td></tr><tr><td>Sample_ID</td><td>Required</td><td>See description in the BCL Convert section</td></tr></tbody></table>
{% endtab %}
{% endtabs %}