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Invalid tag names in VCF: prod & demo #4807

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dnil opened this issue Sep 2, 2024 · 0 comments
Open

Invalid tag names in VCF: prod & demo #4807

dnil opened this issue Sep 2, 2024 · 0 comments

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@dnil
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dnil commented Sep 2, 2024

Describe the issue
Formally starting with VCF v4.3, INFO keys have the restriction:
INFO keys must match the regular expression ^([A-Za-z ][0-9A-Za-z .]*|1000G)$, please note that “1000G” is allowed as a special legacy value.

We have legacy ones on demo, as noted in #4802 and #4803.

2024-08-30 12:20:14 MacBook-Pro-4.local scout.adapter.mongo.hgnc[33662] INFO Building interval trees...
[W::bcf_hrec_check] Invalid tag name: "1000GAF"
[W::bcf_hrec_check] Invalid tag name: "1000G_MAX_AF"
[W::bcf_hrec_check] Invalid tag name: "GERP++_RS_prediction_term"
[W::bcf_hrec_check] Invalid tag name: "1000GAF"
[W::bcf_hrec_check] Invalid tag name: "1000G_MAX_AF"
[W::bcf_hrec_check] Invalid tag name: "GERP++_RS_prediction_term"

For comparison we also have some of these on current MIP prod, and it is not unlikely that there are others out there on other pipes and older cases. Changes should probably be backwards compatible even if it is out of standard , but it can

2024-09-02 07:44:52 hasta.scilifelab.se scout.adapter.mongo.hgnc[120588] INFO Building interval trees...
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/AZ" is invalid, forcing Number=0
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/HW" is invalid, forcing Number=0
[W::bcf_hrec_check] Invalid tag name: "1KGenomesHeteroplasmy"
[W::bcf_hrec_check] Invalid tag name: "1KGenomesHomoplasmy"
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/AZ" is invalid, forcing Number=0
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/HW" is invalid, forcing Number=0
[W::bcf_hrec_check] Invalid tag name: "1KGenomesHeteroplasmy"
[W::bcf_hrec_check] Invalid tag name: "1KGenomesHomoplasmy"

This is a minor issue in the demo file, but it is a bit uncomfortable to realise several keys will have changed names on dbNSFP and similar collections. The old names were used longer in VEP CSQ keys, but will likely change at some point.

To Reproduce
Steps to reproduce the behavior:

  1. run scout setup or scout load case scout/demo/643594.config.yaml
  2. See error

Expected behavior
New renamed keys should be present as synonyms.

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