What is it
The sample sheet is a comma-delimited file (SampleSheet.csv) that stores the information to set up and analyze a sequencing experiment. The file includes a list of samples and their index sequences, as well as the workflow to be employed.
[Header] Date,09/11/2014 Workflow,Amplicon [Manifests] A,truseq_amplicon_cancer_panel_manifest_afp1_pn15032433_b.txt [Settings] AnalysisName,TruSeq Amplicon v1.1 09/11/2014 4:45:37 VariantCaller,Somatic IndelRepeatFilterCutoff,8 AppVersion,220.127.116.11 AppName,TruSeq Amplicon VariantAnnotation,IAS IAS,refseq AnnotationConfig,/opt/App/Plugin/IAS/ProductionAnnotateVCF.exe.config [Data] Sample_ID,Sample_Name,Manifest,GenomeFolder,RunFolder,Lane,Flowcell A1_NA12891_AFP1,NA12891_AFP1,A,/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta,/data/scratch/workspace/10634638_S1_1,1,1
When to use it
Every run in BaseSpace Sequence Hub requires an associated sample sheet to define projects and samples, assign indexes, and run sample sheet driven workflow apps.
When not to use it
Not applicable; you always employ a sample sheet with BaseSpace Sequence Hub.
How to use it
The following table is for reference purposes only. For details about creating or modifying a sample sheet, see the MiSeq Reporter User Guide, MiSeq Sample Sheet Quick Reference Guide, or HiSeq User Guide. You can create a sample sheet using the Illumina Experiment Manager Software.
Table : Sample Sheet Fields
|Investigator Name||(Optional) The name of the investigator.|
|Project Name||(Optional) A descriptive name of the run.|
|Experiment Name||(Optional) A descriptive name of the experiment.|
|Date||The date the sequencing run was performed.|
|Workflow||The analysis workflow for the run.|
|Manifests||This section is only for the Amplicon workflow and is the name of the file (provided by Illumina or created by IEM) used in the Amplicon Workflow. It is required for the Amplicon workflow and ignored by other workflows. The file specifies the alignments to a reference and the targeted reference regions used in the Amplicon workflow.|
|Site Reports||This section is optional and only for the Resequencing and Custom Amplicon workflows. Each line below the SiteReports section header is the name of a SiteReport Input File. This file designates positions on a given chromosome to report the genotype found at that position.|