Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep

Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

http://moonso.github.io/genmod/

MIT License

74 stars 18 forks source link

Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep #105

Open bartcharbon opened 3 years ago

bartcharbon commented 3 years ago

We run Genmod models wit the --vep option.

If the input file in annotated with VEP but one or more lines are missing the CSQ INFO field, Genmod throws an error and aborts: WARNING : genmod.commands.annotate_models: 'CSQ' Aborted!

I understnad that Genmod cannot fully function without the annotation, but it would be nice if this were a warning, so that the other lines in the file can be processed by Genmod

moonso commented 3 years ago

hmm I have to think about this. Since genmod is centered around that variants belong to certain regions I think it is good that it exits if the user says that they are annotated by VEP and then some variants are not. Have you tried to use the genmod annotate regions command and then annotate models without VEP?