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fix: VEP filters away variants too long to annotate #1124

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merged 6 commits into from
Apr 25, 2023
Merged

fix: VEP filters away variants too long to annotate #1124

merged 6 commits into from
Apr 25, 2023

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mathiasbio
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@mathiasbio mathiasbio commented Mar 29, 2023 •
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This PR:

Aims to solve the issue mentioned here: #1123 where SV calls longer than the default max_sv_size are filtered out rather than simple being left un-annotated in the output VCF (in versions > 109 of VEP this was changed so that variants are not filtered out).

Another way to keep all variants, as well as to annotate them, is simply to increase the max_sv_size to the maximum possible size (the size of chromosome 1: 249250621 for hg19, which is larger than chromosome 1 in hg38 and should therefore be fine for both genome versions).

Changed: for changes in existing functionality.

  • Changed --max_sv_size in VEP params to the size of chr1 for hg19.

Tests to be done

  • Install branch on Hasta
  • Run analysis on WGS T / N case hardyweevil
  • Analysis succeeding without errors
  • Variants filtered out from VEP with warning "too long to annotate" are kept in downstream VCF and annotated in case hardyweevil:
    • 24 variants from vep_germline_normal are annotated, not filtered out
    • 42 variants from vep_germline_tumor are annotated, not filtered out
    • 224 variants from vep_somatic_sv are annotated, not filtered out
    • remaining VEP annotations are unchanged

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

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codecov bot commented Mar 29, 2023 •
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Codecov Report

Patch and project coverage have no change.

Comparison is base (9ba7295) 99.31% compared to head (438ce41) 99.31%.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1124   +/-   ##
========================================
  Coverage    99.31%   99.31%           
========================================
  Files           29       29           
  Lines         1756     1756           
========================================
  Hits          1744     1744           
  Misses          12       12
Flag Coverage Δ
unittests 99.31% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
BALSAMIC/constants/workflow_params.py 100.00% <ø> (ø)

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@mathiasbio mathiasbio self-assigned this Mar 29, 2023
@mathiasbio mathiasbio linked an issue Mar 29, 2023 that may be closed by this pull request
SV variants "too long to annotate" from VEP are filtered out #1123
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@mathiasbio mathiasbio mentioned this pull request Mar 29, 2023
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@mathiasbio mathiasbio marked this pull request as ready for review April 21, 2023 07:56
@mathiasbio mathiasbio requested a review from a team April 21, 2023 07:56
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

ivadym
ivadym approved these changes Apr 21, 2023
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🥇

@mathiasbio mathiasbio merged commit c9630fb into develop Apr 25, 2023
@mathiasbio mathiasbio deleted the fix_vep_svsize_filter branch April 25, 2023 09:04
@ivadym ivadym mentioned this pull request Apr 27, 2023
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@mathiasbio mathiasbio mentioned this pull request May 4, 2023
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ivadym added a commit that referenced this pull request May 10, 2023
@ivadym
feat: Release 12.0.0 (#1151)
e4b51ba 
### Added:
* PIP specific missing tools to config #1096
* Filtering script to remove normal variants from TIDDIT #1120
* Store TMB files in HK #1144

### Changed:
* Fixed all conda container dependencies #1096
* Changed --max_sv_size in VEP params to the size of chr1 for hg19 #1124
* Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours #1143
* Update cosmicdb to v97 #1147
* Updated read the docs with the changes relevant to mention #1153

### Fixed:
* Update cryptography version (39.0.1) due to security alert #1087
* Bump cryptography to v40.0.2 and gsutil to v5.23 #1154
* Pytest file saved in balsamic directory #1093
* Fix varcall_py3 container bcftools dependency error #1097
* AscatNgs container #1155
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SV variants "too long to annotate" from VEP are filtered out
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