Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fixes #2057 #2060

Merged
merged 1 commit into from Oct 24, 2023
Merged

fixes #2057 #2060

merged 1 commit into from Oct 24, 2023

Conversation

jemten
Copy link
Collaborator

@jemten jemten commented Oct 23, 2023 •
edited

This PR adds | fixes:

The issue was introduced in MIP 11 with the switch from gatk haplotypecaller to deepvariant. MIP used the sample names found in the vcf from the gatk_variantrecalibration recipe to decode the .mibs file from plink. When the vcf was no longer generated the relatedness checks stopped.

How to test:

  • Automatic and continuous test suite

Expected outcome:

  • Installation, unit and integration test suite pass

Review:

  • Code review
  • Tests pass

This version is a:

  • MAJOR - when you make incompatible API changes. If applicable record manual test results in PR header
  • MINOR - when you add functionality in a backwards compatible manner. If applicable record manual test results in PR header
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

@jemten
Copy link
Collaborator Author

jemten commented Oct 23, 2023

<case_id>_qc_sample_info.yaml file prior to MIP 11

...
  pedigree_check:
    path: /home/proj/stage/rare-disease/mip/validation/20200428/justhusky/analysis/justhusky/gatk_variantrecalibration/justhusky_gent_vrecal.vcf
...

With the fix

...
  pedigree_check:
    path: /home/proj/stage/rare-disease/cases/justhusky/analysis/justhusky/plink/justhusky_gatkcomb_no_indels_ann_uniq.vcf
...

@jemten jemten marked this pull request as ready for review October 23, 2023 17:19
@jemten jemten requested review from henrikstranneheim and a team as code owners October 23, 2023 17:19
@jemten jemten linked an issue Oct 23, 2023 that may be closed by this pull request
Relation_check not working #2057
Closed
henrikstranneheim
henrikstranneheim approved these changes Oct 24, 2023
View reviewed changes
Copy link
Collaborator

@henrikstranneheim henrikstranneheim left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

👍

@jemten jemten merged commit 443391f into master Oct 24, 2023
9 checks passed
@jemten jemten deleted the release/12.0.2 branch October 24, 2023 07:10
@jemten jemten restored the release/12.0.2 branch October 24, 2023 07:10
@jemten jemten deleted the release/12.0.2 branch October 24, 2023 10:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@henrikstranneheim henrikstranneheim henrikstranneheim approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Relation_check not working
2 participants
@jemten @henrikstranneheim