GPL-659 Filter out high CT & limit of detection samples about lighthouse

[rl15]

Jeff B wrote (Tuesday, 8 September 2020 at 08:31)

For picking samples the key data will be the Cq values from the first 3 channels (which are the SARS-CoV2 test PCR products). However, it is helpful to know the positive control (channel 4) and the calls they make as part of our ongoing comparisons, so if it is not too difficult for the LIMS team to add those as well, then I think that is safest. Finally, the Target columns are obviously hugely redundant, and so the only reason for keeping them is to be able to track if the lab changes their target, or to compare across labs which may have different targets (indeed, I think Cambridge may only use one?).

[rl15]

Rich L wrote (Friday, 25 September 2020 at 17:28)

Can you check my understanding below for the CT value features, 1) parsing + persisting data and 2) filtering samples out of positive report

...

Remove sample from pick list when following rule fires

High CT rule: Remove sample when one or more of CH1-Cq, CH2-Cq or CH3-Cq values > 29?

Q. Will CT threshold be the same for all labs?

[rl15]

Jeff B wrote (Monday, 28 September 2020 at 12:39)

The rule should fire if all non-missing channels are > 30. (CH1-Cq > 30 && CH2-Cq > 30 && CH3-Cq > 30)
Threshold will be same for all labs, though if one lab provides fewer than three channels, it applies to as many as there are.

[KatyTaylor]

To test this and related stories (#126, #129):

In UAT:

• Make sure have deployed Andrew's stories (sanger/crawler#108 etc.)
• Wait until some samples are imported by nightly crawler that have Ct values, or create some dummy samples in the MongoDB - we want a mix of:
  • positive samples with no Ct value data
  • positive samples with Ct values > 30
  • positive samples with Ct values < 30
  • positive samples with mixed Ct values
  • positive samples where Root Sample ID starts with 'CBIQA_'
• Run the Lighthouse 'positives on site report' & check that some samples are filtered out based on correct criteria
• Scan plate barcodes of some of above samples into UAT LabWhere
• Run Lighthouse Sentinel Sample Creation and check samples are imported based on same correct criteria