Is your feature request related to a problem? Please describe.
Jannovar picks transcript by the most severe consequences of transcript. But there are genes that overlapped with each other and with the same consequences. If report only one gene of information may lost the very critical information . For example, X: 101399747 is a very important position for several diseases. But Jannovar reports RPL36A-HNRNPH2 instead of the disease-causative gene GLA (vcf mode).
Describe the solution you'd like
I know that the --show-all could solve this problem, but the data size become very big. So I would recommend that report variants by gene.
Assume GeneA and GeneB are overlapped with each other and Transcript1, Transcript2 and Transcript3 have the same consequences.
Jannovar may just random pick one of transcript(I guess). I recommend to report (Transcript1 or Transcirpt2) and (Transcript3). Then, the information of GeneA and GeneB will be reported, respectively.
GeneA Transcript1
GeneA Transcript2
GeneB Transcript3
Describe alternatives you've considered
N/A
Additional context
Example of genes that overlapped with each other.
Is your feature request related to a problem? Please describe.
Jannovar picks transcript by the most severe consequences of transcript. But there are genes that overlapped with each other and with the same consequences. If report only one gene of information may lost the very critical information . For example, X: 101399747 is a very important position for several diseases. But Jannovar reports RPL36A-HNRNPH2 instead of the disease-causative gene GLA (vcf mode).
Describe the solution you'd like
I know that the --show-all could solve this problem, but the data size become very big. So I would recommend that report variants by gene.
Assume GeneA and GeneB are overlapped with each other and Transcript1, Transcript2 and Transcript3 have the same consequences.
Jannovar may just random pick one of transcript(I guess). I recommend to report (Transcript1 or Transcirpt2) and (Transcript3). Then, the information of GeneA and GeneB will be reported, respectively.
GeneA Transcript1
GeneA Transcript2
GeneB Transcript3
Describe alternatives you've considered
N/A
Additional context
Example of genes that overlapped with each other.