Parameters
The following fields are available for use with the sample sheet v2 template. Different sequencing systems can support different parameters or expect certain values in the sample sheet. Refer to the settings for your specific system.
Standalone Sections
Header Section parameters
Parameter | Description | Requirements |
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Custom_* | Custom field used to capture run metadata. | String with ASCII characters except for * and the control characters CR and LF. |
FileFormatVersion | 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. | Must always be 2. |
InstrumentPlatform | Identifies the instrument platform to be used for the run. For example, NextSeq1000 or NextSeq2000. | String with ASCII characters except for * and the control characters CR and LF. |
InstrumentType | Identifies the instrument to be used for the run. For example: if using NextSeq 2000, populate the field with NextSeq2000. | String with ASCII characters except for * and the control characters CR and LF. |
RunDescription | The run description can contain 255 alphanumeric characters, spaces, dashes, and underscores. | String with ASCII characters except for * and the control characters CR and LF. |
RunName | The run name can contain 255 alphanumeric characters, spaces, dashes, and underscores. | String with ASCII characters except for * and the control characters CR and LF. |
Reads Section Parameters
Parameter | Description | Requirements |
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Index1Cycles | Number of cycles in Index Read 1. Required if more than one sample is present in sample sheet. |
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Index2Cycles | Number of cycles in Index Read 2. Required if using dual indexes for demultiplexing. |
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Read1Cycles | Number of cycles for Read 1. |
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Read2Cycles | Number of cycles for Read 2. Required only when running a paired-end sequencing run. |
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Sequencing Section Parameters
Parameter | Description | Requirements |
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CustomIndex1Primer | Indicates if a Custom Index 1 primer is used for the run. | Values |
CustomIndex2Primer | Indicates if a Custom Index 2 primer is used for the run. | Values |
CustomRead1Primer | Indicates if a Custom Read 1 primer is used for the run. | Values |
CustomRead2Primer | Indicates if a Custom Read 2 primer is used for the run. | Values |
LibraryPrepKits | Identifies the library prep kit used for the run. |
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Application Sections
Application Section Parameters
Parameter | Description | Requirements |
AdapterRead1 | The sequence of the Read 1 adapter to be masked or trimmed. | Possible values are a concatenation from the set [A,C,T,G] and additional values based on your instrument. To trim multiple adapters, separate the sequences with a plus sign (+) indicating independent adapters that must be independently assessed for masking or trimming for each read. |
AdapterRead2 | The sequence of the Read 2 adapter to be masked or trimmed. | Possible values are a concatenation from the set [A,C,T,G], and additional values based on your instrument. To trim multiple adapters, separate the sequences with a plus sign (+) indicating independent adapters that must be independently assessed for masking or trimming for each read. |
AppVersion | The version of the workflow-specific application (for example, DRAGEN Enrichment). | Use all three integers included in the version name. For example, 1.0.0. |
AuxCnvPanelOfNormalsFile | File name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. |
AuxCnvPopBAlleleVcfFile | File name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. Optional if VariantCallingMode is The value must be CNV output is only be generated if this file is provided. |
AuxGermlineTaggingFile | File name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. The value must be Germline tagging output is only be generated if this file is provided. |
AuxNoiseBaselineFile | File name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. For the DRAGEN Enrichment and DRAGENSomatic, applicable only if For more information on noise baseline files, refer to the instrument product documentation. The value must be |
AuxSvNoiseBaselineFile | File name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. Optional if VariantCallingMode is The value must be |
BarcodeMismatchesIndex1 | Specifies barcode mismatch tolerance for Index 1. | Possible values are 0, 1, or 2. Additional values might be available based on your instrument. The default value is 1. Only allowed if Index 1 is specified in |
BarcodeMismatchesIndex2 | Specifies barcode mismatch tolerance for Index 2. | Possible values are 0, 1, or 2. Additional values might be available based on your instrument. The default value is 1. Only allowed if Index 2 is specified in |
BarcodePosition | The location of the bases that corresponds to the barcode within the value entered for | For DRAGEN Single Cell Library Kits 1–5, enter the BarcodePosition value in the following format:
For example, if a barcode contains 16 bases, the value is For DRAGEN Single Cell Library Kits 6, enter the
For example, the following structure would result in the value
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BarcodeRead | The locations within the sequencing run of the barcode read that contains both the barcode and the UMI. | Values can contain |
BarcodeSequenceList | The name of the file containing the barcode sequences to include. | The file name can only contain alphanumeric characters, dashes, underscores, and periods. |
Bedfile | BED file to be used for analysis in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. |
Comparison1 | Comparison sample 1. |
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Comparison2 | Comparison sample 2. |
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Comparison3 | Comparison sample 3. |
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Comparison4 | Comparison sample 4. |
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Comparison5 | Comparison sample 5. |
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CreateFastqForIndexReads | If set to
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DifferentialExpressionEnable | Enable or disable differential expression for DRAGEN RNA. |
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DnaBedFile | The BED file containing the regions to target. The BED file can be input in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. |
DnaGermlineOrSomatic | To perform DNA Amplicon germline analysis, enter | Accepted values are |
DnaOrRna | The type of Amplicon analysis to perform. | Only DNA analysis is supported for DRAGENv3.8. Enter |
DownSampleNumReads | Specifies the number of fragments to downsample to. For paired-end sequencing, the number of reads at the down-sampling output is twice the number of fragments specified. |
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FastqCompressionFormat | The compression format for the FASTQ output files. Example values are | The value |
GermlineOrSomatic | Specifies either enrichment germline analysis or enrichment somatic analysis. | Accepted values are |
Index | The Index 1 (i7) index adapter sequence. |
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Index2 | The Index 2 (i5) Index adapter sequence. |
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KeepFastQ | Indicates whether FASTQ files are saved ( | Accepted values are |
Lane | Specifies FASTQ files only for the samples with the specified lane number. | Must adhere to the following requirements:
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MapAlignOutFormat | Formatting of the alignment output files. | Accepted values are |
MethylationProtocol | Select the library protocol for methylation analysis. | Accepted values are |
OverrideCycles | Specifies the sequencing and indexing cycles to be used when processing the sequencing data.
For instruments with Example of 8 bp i5 index with the last two (adapter) bases to be trimmed where XX is part of the adapter sequence.
Although Index2 is processed on the instrument in reverse complement format, Index2 and OverrideCycles are entered in the sample sheet in forward, non-complemented format for user convenience. | Must adhere to the following requirements:
The following are examples of OverrideCycles input:
For a sample sheet containing two samples having the following OverrideCycles, the number of cycles used for demultiplexing sums to 18:
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QcCoverage1BedFile | File name in text (*.txt) or gzip (*.gz) format. | Must include the prefix If QcCoverage1BedFile exists in the Data section, but a file is not provided, you must specify a value of |
QcCoverage2BedFile | File name in text (*.txt) or gzip (*.gz) format. | Must include the prefix If QcCoverage2BedFile exists in the Data section, but a file is not provided, you must specify a value of |
QcCoverage3BedFile | File name in text (*.txt) or gzip (*.gz) format. | Must include the prefix If QcCoverage3BedFile exists in the Data section, but a file is not provided, you must specify a value of |
QcCrossContaminationVcfFile | File name in text (*.txt) or gzip (*.gz) format. | Must include the prefix If QcCrossContaminationVcfFile exists in the Data section, but a file is not provided, you must specify a value of |
ReferenceGenomeDir | The reference genome name. | Alphanumeric string with underscores (_) or dashes (-). To use a custom reference genome, refer to Reference Builder for Illumina Instruments v1.0.0 App Online Help. |
RnaGeneAnnotationFile | Genotype reference file name in text (*.txt) or gzip (*.gz) format. | Alphanumeric string with underscores (_) or dashes (-) or periods (.) with no spaces allowed. If DifferentialExpressionEnable is |
RnaLibraryType | Identifies if the RNA library type is stranded forward, stranded reverse, or unstranded. | Enter one of the following values:
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RnaPipelineMode | Identifies the pipeline mode as | Accepted values are |
Sample_ID | ID for the sample. | Must adhere to the following requirements:
It is recommended to separate each identifier with a dash. For example, For BCL Convert, the same sample ID can exist on more than one row of the sample sheet to indicate one sample spanning more than one lane. For non BCL Convert workflows, a unique sample ID can only appear in one non BCL Convert workflow. No workflows allow |
Sample_Name | Use | Can only contain alphanumeric characters, dashes, and underscores. Duplicate data strings with different cases (for example, |
Sample_Project | If present, and both | Can only contain alphanumeric characters, dashes, and underscores. Duplicate data strings with different cases (for example, |
SoftwareVersion | For the BCL Convert application, the version of software used to perform BCL conversion on sample IDs that only exist in the BCL Convert Data section. For other application sections, identifies the version of the DRAGEN software to be used process the specific DRAGEN pipeline, including conversion to FASTQ. | Use all three integers included in the DRAGEN version name. For example, 3.5.7. |
TrimUMI | If set to false or 0, UMI sequences are not trimmed from output FASTQ reads. The UMI is still placed in sequence header. |
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UmiPosition | The location of the bases that corresponds to the UMI within the value entered for BarcodeRead. | Enter the
For example, if the UMI contains 10 bases and the barcode contains 16, the value is |
UsesTaps | Select whether the TAPS assay, which directly converts methylated C to T, is used ( | Accepted values are true or false. |
VariantCallingMode | Variant calling mode for the run. | Accepted values are DRAGEN Version 4.1.7 includes CYP2B6, CYP21A2, SMN, and GBA. For DRAGEN Enrichment and DRAGENSomatic, the option for all variant callers includes Small, Structural, and CNV callers (if panel of normals is provided). |
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