VADR produces qualifier with invalid value about vadr HOT 4 OPEN

This is what is desired:

Qualifier       /ribosomal_slippage
Definition      during protein translation, certain sequences can program
                ribosomes to change to an alternative reading frame by a 
                mechanism known as ribosomal slippage 
Value format    none 
Example         /ribosomal_slippage 
Comment         a join operator,e.g.: [join(486..1784,1787..4810)] should be used 
                in the CDS spans to indicate the location of ribosomal_slippage 

from vadr.

That's actually a different format than the .tbl file that vadr creates, despite them both being (confusingly) called feature tables. The format of vadr output 'feature tables' is described here: https://www.ncbi.nlm.nih.gov/genbank/feature_table/

The vadr format is a useful file format for submissions to GenBank. There may be ways to convert it to a format that ENA accepts for submissions, but I'm not sure what those formats are. The vadr .ftr output files may also be relatively easy to parse and reformat into an accepted ENA format.

from vadr.

Hi @nawrockie ,

I've so far used VADR to submit nine CoV genomes to ENA with remote homology to SARS-CoV-2. The latest version of DARTH will have the scripts to turn VADR output into a format that can be submitted to ENA using their Webin-CLI tool.

I looked at the GenBank feature_table page, but it doesn't talk about ribosome slippage, and how to encode it correctly (the page seems to be more concerned about syntax). INSDC is a collaboration between GenBank, DDBJ, and EMBL, so why wouldn't the semantics defined for INSDC apply to the GenBank?

from vadr.

VADR outputs the .tbl file format because that was preferred by the GenBank indexers for viral submissions at the time of development. In the GenBank submission pipeline, the vadr .tbl format file is then converted to 'asn' format using tbl2asn which is used to input the data into the GenBank database.

The latest version of DARTH will have the scripts to turn VADR output into a format that can be submitted to ENA using their Webin-CLI tool.

That sounds good. Have you finished developing the format conversion tool/script, or do you still have a problem with ribosomal_slippage?

from vadr.