Currently, the TSV conversion produces TSV files having each feature annotation of a variant (e.g., a transcript) as separate row.
This produces a TSV file in which a specific variant can be reported multiple times, e.g., if multiple transcripts are reported or a transcript and a regulatory region are affected by this variant.
With the current transcript filtering, e.g. by the PICK flag, a large number of variants are reported with multiple feature annotation.
Hence, I suggest to change the TSV conversion to produce only one row per variant.
Further, the transcript filtering process should be revised to prioritze one "major" feature annotation to be displayed on front and show alternative feature annotations as separate columns.
This makes the report smaller especially if a large list of transcripts is kept and also more clear, as it summarizes all consequences of the variant that otherwise could get lost due to specific filter settings.
This requires substantial changes probably associated with a new major release.
vembrane ist currently not capable of performing this TSV conversion and might need an update or replacement for this process.
a process for choosing the "major" feature annotation needs to be established. This needs to deal with ambiguous cases in which multiple feature annotations are selected by the current process.
making sure that altenative transcript annotations are still considered for the subsequent custom filters.
Description of feature
Currently, the TSV conversion produces TSV files having each feature annotation of a variant (e.g., a transcript) as separate row. This produces a TSV file in which a specific variant can be reported multiple times, e.g., if multiple transcripts are reported or a transcript and a regulatory region are affected by this variant. With the current transcript filtering, e.g. by the PICK flag, a large number of variants are reported with multiple feature annotation.
Hence, I suggest to change the TSV conversion to produce only one row per variant. Further, the transcript filtering process should be revised to prioritze one "major" feature annotation to be displayed on front and show alternative feature annotations as separate columns.
This makes the report smaller especially if a large list of transcripts is kept and also more clear, as it summarizes all consequences of the variant that otherwise could get lost due to specific filter settings.
This requires substantial changes probably associated with a new major release.
vembraneist currently not capable of performing this TSV conversion and might need an update or replacement for this process.