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umccr / umccrise

:snake: DRAGEN Tumor/Normal workflow post-processing
https://umccr.github.io/umccrise/
MIT License
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CPSR: convert predisposition genes to Ensembl Gene IDs #126

Closed pdiakumis closed 10 months ago

pdiakumis commented 1 year ago

The newer (v1) CPSR version uses Ensembl Gene IDs instead of gene symbols:

psr-validate-input-arguments - ERROR -
Custom list of genes from CPSR superpanel (panel 0) should be provided as Ensembl gene identifiers, 'AIP' is not a valid identifier

This has been tackled in the genes_update branch of https://github.com/umccr/NGS_Utils, just need to merge that PR.

See relevant Slack discussion.

Note that we cannot at this stage insert custom genes since they need to come from the CPSR superpanel, so 3 of the 78 genes we've been using (CSDE1, EGLN1, and EGLN2) will not be queried in the CPSR report.

pdiakumis commented 1 year ago

Make sure the Ensembl version used is in harmony. See #134.

pdiakumis commented 10 months ago

See Slack discussion in https://umccr.slack.com/archives/C04TD8QJG3W/p1680011173372029