Audit LUCA-KR

[hknahal]

Breakdown of 1,571 donors showing in Program Dashboard:

156 samples need to removed at request of program (will be addressed in this ticket: https://github.com/icgc-argo/workflow-roadmap/issues/267): https://docs.google.com/spreadsheets/d/1ggshqQS9c40nPizDjxuhEG7hHdyvDCSZ/edit#gid=425884767

• 2 donors are published in SONG (highlighted in red in the table) -> these will need to suppressed.
• Remaining 154 donors can be deleted from clinical
• NOTE: During auditing, 2 donors were discovered to have values in the submitter_specimen_id field which include commas (highlighted in yellow). The regex in the dictionary should have prevented this, so unclear how these got validated. Created a separate ticket to address this: https://github.com/icgc-argo/argo-dictionary/issues/405

An additional 1,248 donors have discrepancies that will need to followed up with program: https://docs.google.com/spreadsheets/d/1ggshqQS9c40nPizDjxuhEG7hHdyvDCSZ/edit#gid=902346357

• Program submitted two different submitter_donor_ids for tumour and normal samples belonging to the same donor.
• 312 donors are published in SONG (highlighted in red) -> these will need to be suppressed.

167 donors were imported from ICGC25K: https://docs.google.com/spreadsheets/d/1ggshqQS9c40nPizDjxuhEG7hHdyvDCSZ/edit#gid=60315048

• No action required

[edsu7]

Jon will reindex the data.

[edsu7]

Multiple issues

• regex for submitterSpecimenId will be addressed and fixed in dictionary release 1.19
• data submitter using submitterSpecimenId as submitterDonorId, @hknahal will share list of discrepancies with data submitter to verify. Followed up with deletion and resubmission.
• Also confirm if molecular data has been processed. If so, will have to reindexing data reflecting new IDs

[hknahal]

@lindaxiang @edsu7 Closing this ticket since 156 donors were removed. Followed up with data submitter regarding 1,248 donors with submitter_donor_id discrepancies. Can create a separate ticket for this once data submitter confirms issue and whether they want to have them deleted.

[lindaxiang]

@edsu7 can you add update?

[justincorrigible]

Superseded by https://github.com/icgc-argo/workflow-roadmap/issues/395