ccrcc_wcm_2022 study

[Rima-Waleed]

What?

Adding new public study: ccrcc_wcm_2022

checks

For all pull requests:

• Passes validation

For a new study (in addition to above):

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• is study meta data complete? e.g. pmid, group of PUBLIC
• were all samples profiled with WES/WGS? If not, is gene panel file curated?
• are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• clinical sample and patient data with meta files
• mutations data with meta files
• MAF is based on hg19
• MAF with 2 isoforms: uniprot and mskcc
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Case-lists for all profiles.
• Manual checking (Niki or JJ): Triage or private Portal link here

[inodb]

Preview import failure

Tried to import public/ccrcc_wcm_2022 into hub.cbioportal.org and the mutations step failed with a duplicate primary key:

DB Error: only 65224 of the 65802 records were inserted in `mutation_event`.
Duplicate entry '497' for key 'mutation_event.PRIMARY'

Likely two rows in data_mutations.txt describe the same variant (same chromosome / start / end / ref / alt / gene). Deduping that file should unblock the import.