SampleSheet.csv

Illumina SequencingRuns have a file called “SampleSheet.csv” which lists the sample names, barcodes and other info.

VG stores this as a SampleSheet model, with SequencingSample representing each rows. This is eventually linked through FastQ/Bams etc to VCF samples

Many years ago we noticed the SampleSheet was the main handover point between wet and dry lab staff, so have been adding extra columns to annotate our samples (such as kits, patient record codes etc)

VariantGrid allows storing key/values for a SequencingSample in SequencingSampleData

Because the columns are highly specific to each lab/disk setup, the core code raises a sequencing_run_sample_sheet_created_signal signal, which lab/deployment specific code can listen for and run

CurrentSampleSheet

People often modify sample sheets, to correct sample names etc. We reload SampleSheets (re-sent via API or reloaded in scan due to modification date/hash)

SequencingRuns can have many SampleSheets but only one CurrentSampleSheet - which represents the one on the disk, that was most recently used to generate downstream files

When a SampleSheet is assigned to a sequencing run (1st time, or later modifications) the signal sequencing_run_current_sample_sheet_changed is raised

SA Pathology Special Columns

Panel , PanelVersion - These are used to create an EnrichmentKit if it doesn’t exist, and assign it to SequencingSample. If all samples are assigned to the same kit, the SequencingRun is also assigned to that kit. SA Path VG deployment handles via listening for sequencing_run_sample_sheet_created_signal and handling via sapath.signals.sapath_enrichment_kits.sapath_sample_sheet_created_handler

SAPOrderNumber - These are de-identified codes used to represent a pathology test order. We can use this to link up to our LIMS/Medical record system patient information (Helix). SA Path code listens for sequencing_run_current_sample_sheet_changed_handler signal, handles via sapath.signals.sample_sap_order_matching.sapath_sequencing_run_current_sample_sheet_changed_handler