> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/run-set-up/overview/resources/bcl-convert-parameter-usage.md).

# BCL Convert Parameter Usage

In this section, we highlight various desired outcomes and provide examples to show how they can be achieved.

{% hint style="info" %}
For more information on how to use each parameter, see the [Instrument Settings](/run-set-up/overview/instrument-settings.md) guide.
{% endhint %}

<table data-full-width="true"><thead><tr><th>Desired Outcome</th><th>Example</th></tr></thead><tbody><tr><td>Adapter Matching Algorithm</td><td>FindAdaptersWithIndels,true <em>(default off, false = Sliding Window)</em></td></tr><tr><td>Adapter Read 1, 2 Masking</td><td>AdapterRead1,A/T/C/G AdapterRead2,A/T/C/G AdapterBehavior,mask <em>(default trim)</em></td></tr><tr><td>Adapter Read 1, 2 Trimming</td><td>AdapterRead1,A/T/C/G AdapterRead2,A/T/C/G AdapterBehavior,trim <em>(default trim)</em></td></tr><tr><td>Adapter Stringency</td><td>AdapterStringency,# <em>(default 0.9, 0.5-1.0 allowed)</em></td></tr><tr><td>Barcode Collision Checks</td><td><p>Depending on version, index collision checks are relaxed, strict, or configurable:</p><ul><li>3.9.x: Relaxed by default, no option to change. A collision in one index can be rescued by having enough diversity in the combined dual index sequence.</li><li>v3.10 and 4.0: Strict by default, no option to change. For a dual index run, requires only 1 index (index1 or index2) to have a collision in order to error out based on a barcode collision. Identical indexes within index1 or index2 (combinatorial dual indexes) still supported.</li><li>4.1.5: Strict by default but configurable to relaxed mode using sample sheet option:</li></ul><p>CombinedIndexCollisionCheck,value Where value corresponds to the number of the lane or lanes to use this behavior; multiple lane values should be semicolon-separated.</p><ul><li>4.1.7 and 4.2.x: Relaxed mode by default. CombinedIndexCollisionCheck removed. Mode now configured by using sample sheet option:</li></ul><p>IndependentIndexCollisionCheck,value to allow optional strict checking, where value corresponds to the number of the lane or lanes to use this behavior; multiple lane values should be semicolon-separated.</p></td></tr><tr><td>Barcode Mismatches</td><td>BarcodeMismatchIndex1,# <em>(default 1)</em> BarcodeMismatchIndex2,# <em>(default 1)</em></td></tr><tr><td>Combine multiple FASTQ files</td><td>NoLaneSplitting,true or false <em>(default false)</em></td></tr><tr><td>Ignore beginning or end of read</td><td>OverrideCycles,Y#;N# <em>(default all cycles used)</em><br><br>Note: OverrideCycles can be specified in the BCL Convert Settings section to be applied globally or in the BCL Convert Data section to be applied uniquely per-sample.</td></tr><tr><td>Index FASTQs</td><td>CreateFastqForIndexReads, 0 or 1 <em>(default 0)</em></td></tr><tr><td>Minimum Number of ATCG Bases per Read</td><td>MaskShortReads,# <em>(default 22)</em></td></tr><tr><td>Minimum Read Length</td><td>MinimumTrimmedReadLength,# <em>(default 35)</em></td></tr><tr><td>Trimming last bases when they match the adapter</td><td>MinimumAdapterOverlap,# <em>(default 1, 1-3 allowed)</em> Never trims or masks less than X bases when they overlap with the adapter provided regardless of stringency settings, where X is the MinimumAdapterOverlap provided.</td></tr><tr><td>UMI Settings</td><td>OverrideCycles,U# TrimUMI,0 or 1 <em>(default 1)</em></td></tr><tr><td>Use a subset of bases for i7/i5 indexes</td><td>Use subset of index cycles for demultiplexing by providing shortened sequence in index or index2 column and providing desired length in OverrideCycles setting <em>(default use all index cycles defined in RunInfo.xml)</em></td></tr></tbody></table>


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