BCL Convert Parameter Usage

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

For more information on how to use each parameter, see the Instrument Settings guide.

Desired Outcome	Example
Adapter Matching Algorithm	FindAdaptersWithIndels,true (default off, false = Sliding Window)
Adapter Read 1, 2 Masking	AdapterRead1,A/T/C/G AdapterRead2,A/T/C/G AdapterBehavior,mask (default trim)
Adapter Read 1, 2 Trimming	AdapterRead1,A/T/C/G AdapterRead2,A/T/C/G AdapterBehavior,trim (default trim)
Adapter Stringency	AdapterStringency,# (default 0.9, 0.5-1.0 allowed)
Barcode Collision Checks	Depending on version, index collision checks are relaxed, strict, or configurable: 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. 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. 4.1.5: Strict by default but configurable to relaxed mode using sample sheet option: CombinedIndexCollisionCheck,value Where value corresponds to the number of the lane or lanes to use this behavior; multiple lane values should be semicolon-separated. 4.1.7 and 4.2.x: Relaxed mode by default. CombinedIndexCollisionCheck removed. Mode now configured by using sample sheet option: 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.
Barcode Mismatches	BarcodeMismatchIndex1,# (default 1) BarcodeMismatchIndex2,# (default 1)
Combine multiple FASTQ files	NoLaneSplitting,true or false (default false)
Ignore beginning or end of read	OverrideCycles,Y#;N# (default all cycles used) 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.
Index FASTQs	CreateFastqForIndexReads, 0 or 1 (default 0)
Minimum Number of ATCG Bases per Read	MaskShortReads,# (default 22)
Minimum Read Length	MinimumTrimmedReadLength,# (default 35)
Trimming last bases when they match the adapter	MinimumAdapterOverlap,# (default 1, 1-3 allowed) 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.
UMI Settings	OverrideCycles,U# TrimUMI,0 or 1 (default 1)
Use a subset of bases for i7/i5 indexes	Use subset of index cycles for demultiplexing by providing shortened sequence in index or index2 column and providing desired length in OverrideCycles setting (default use all index cycles defined in RunInfo.xml)