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molgenis
Variant Interpretation Pipeline
**Describe the bug** A clear and concise description of what the bug is. **To Reproduce** 1. Run test suite and inspect `test_sv` results output: [sv.vcf.gz](https://github.com/molgenis/vip/files/8946301/sv.vcf.gz) capice annotation output: [sv_chunk0_capice_output.tsv.gz](https://github.com/molgenis/vip/files/8946302/sv_chunk0_capice_output.tsv.gz) **Expected...
**Describe the bug** A clear and concise description of what the bug is. **To Reproduce** Steps to reproduce the behavior: 1. Go to '...' 2. Click on '....' 3. Scroll...
``` running tests ... vcf/aip | PASSED | 230423=completed test/output/vcf/aip/.nxf.log vcf/chd7 | PASSED | 230424=completed test/output/vcf/chd7/.nxf.log vcf/corner_cases | PASSED | 230425=completed test/output/vcf/corner_cases/.nxf.log vcf/deb_register | PASSED | 230426=completed test/output/vcf/deb_register/.nxf.log vcf/empty_input |...
see https://github.com/molgenis/vip/blob/v7.7.1/resources/field_metadata.json#L98 ``` []$ zcat resources/GRCh38/clinvar_20240603_stripped.tsv.gz | tail -n+2 | cut -f 6 | sort | uniq -c ``` ``` 1360362 Uncertain_significance 875295 Likely_benign 202876 Benign 158012 Pathogenic 125831 Conflicting_classifications_of_pathogenicity...
Caused by https://github.com/Ensembl/ensembl-vep/issues/1598 Can cause test failures: ``` running tests ... vcf/aip | PASSED | 226457=completed test/output/vcf/aip/.nxf.log vcf/chd7 | PASSED | 226458=completed test/output/vcf/chd7/.nxf.log vcf/corner_cases | PASSED | 226459=completed test/output/vcf/corner_cases/.nxf.log vcf/deb_register...
End-to-end tests are not executed by Travis CI, please execute manually: - [ ] `APPTAINER_BIND=$PWD bash test/test.sh` passes - [ ] Updated documentation
End-to-end tests are not executed by Travis CI, please execute manually: - [ ] `APPTAINER_BIND=$PWD bash test/test.sh` passes - [ ] Updated documentation
End-to-end tests are not executed by Travis CI, please execute manually: - [ ] `APPTAINER_BIND=$PWD bash test/test.sh` passes - [ ] Updated documentation
``` running tests ... vcf/aip | PASSED | 339915=completed test/output/vcf/aip/.nxf.log vcf/chd7 | PASSED | 339916=completed test/output/vcf/chd7/.nxf.log vcf/corner_cases | PASSED | 339917=completed test/output/vcf/corner_cases/.nxf.log vcf/deb_register | PASSED | 339918=completed test/output/vcf/deb_register/.nxf.log vcf/empty_input |...