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

Fix CTX END2 error in GATK formatting script #557

Merged
merged 1 commit into from
Jun 23, 2023
Merged

Fix CTX END2 error in GATK formatting script #557

merged 1 commit into from
Jun 23, 2023

Conversation

mwalker174
Copy link
Collaborator

Addresses a bug introduced in #540 that causes the following kind of error in the GATK formatting script:

Traceback (most recent call last):
  File "/opt/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py", line 239, in <module>
    main()
  File "/opt/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py", line 235, in main
    _process(vcf_in, vcf_out, arguments)
  File "/opt/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py", line 193, in _process
    out = convert(record=record, bnd_end_dict=bnd_end_dict,
  File "/opt/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py", line 131, in convert
    record.info['END2'] = bnd_end_dict[record.id] if bnd_end_dict is not None \
KeyError: 'ref_panel_1kg.chr2.final_cleanup_CTX_chr2_1'

This occurred specifically for CTX records when attempting to update the END2 field. This update has been tested on an offending VCF.

epiercehoffman
epiercehoffman approved these changes Jun 22, 2023
View reviewed changes
Copy link
Collaborator

@epiercehoffman epiercehoffman left a comment

Choose a reason for hiding this comment

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

LGTM

@mwalker174 mwalker174 merged commit 2fdf7af into main Jun 23, 2023
@mwalker174 mwalker174 deleted the mw_format_end2_fix branch June 23, 2023 15:28
gatk-sv-bot pushed a commit to Genometric/gatk-sv that referenced this pull request Jun 27, 2023
@mwalker174 @gatk-sv-bot
Fix CTX END2 error in GATK formatting script (broadinstitute#557)
dde5ad5
gatk-sv-bot pushed a commit to Genometric/gatk-sv that referenced this pull request Jun 27, 2023
@mwalker174 @gatk-sv-bot
Fix CTX END2 error in GATK formatting script (broadinstitute#557)
941ce97
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@epiercehoffman epiercehoffman epiercehoffman 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.
2 participants
@mwalker174 @epiercehoffman