Description
When running the small test SV VCF through the SV postprocessing workflow the VCF after the VEP stage is empty. After looking in the warninglog for VEP I saw this for each variant in the VCF:
WARNING: line 1 skipped (9 20414424 0 C C]11:118355689] 67 PASS ASMID=4...): Chromosome 9 not found in annotation sources or synonyms; chromosome 9 does not overlap any features
WARNING: line 2 skipped (9 20414999 1 C [11:118355716[C 74 PASS ASMID=2...): Chromosome 9 not found in annotation sources or synonyms; chromosome 9 does not overlap any features
WARNING: line 3 skipped (11 118355689 2 A A]9:20414424] 67 PASS ASMID=4...): Chromosome 11 not found in annotation sources or synonyms; chromosome 11 does not overlap any features
...
How to reproduce
Check the final SV VCF from the current test in oncorefiner.
Expected behaviour
All variants regardless of if they can be annotated or not should be preserved in the VCF
Anything else?
In balsamic we're running VEP with a few extra settings such as "--allow_non_variant --dont_skip" which might be what we need to add to tell VEP not to remove these variants. http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
System information
No response
Description
When running the small test SV VCF through the SV postprocessing workflow the VCF after the VEP stage is empty. After looking in the warninglog for VEP I saw this for each variant in the VCF:
How to reproduce
Check the final SV VCF from the current test in oncorefiner.
Expected behaviour
All variants regardless of if they can be annotated or not should be preserved in the VCF
Anything else?
In balsamic we're running VEP with a few extra settings such as "--allow_non_variant --dont_skip" which might be what we need to add to tell VEP not to remove these variants. http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
System information
No response