Collecting refseq versions to build improved clinvar submission files

[northwestwitch]

This is not so easy, but in order to submit complete info via clinvar variant submission files we need to add the refseq version to the submission. So far we save in Scout just the refseq code. Maybe it's easily fixable by querying some external database on the fly..

[northwestwitch]

I forgot to add that if users decide to add a refseq code (and they have to) without specifying the version, then the submission is rejected until they don't add the missing field.

[henrikstranneheim]

Here is a flat file with a genbank=NM.version that one can use: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz

One could add this to the VEP annoation, and I will look into if I can include this in the MIP analysis. Other option is to add this to Scouts internal database of transcripts.

[northwestwitch]

Thanks @henrikstranneheim. We could meet to discuss about this with @moonso as well, who knows best how transcripts and refseq are saved in scout db.

[henrikstranneheim]

MIP 7.0 now uses VEPs merged cash to add the refseq transcript version which can then be picked up by Scout in the CSQ field. @northwestwitch There was another field required as well which scout do not have right? Was it the refseq for the entire build?

[northwestwitch]

It was just that I think, the other problem was much simpler to fix, see #901

[henrikstranneheim]

Excellent! Thx

[northwestwitch]

Thank you! :)

[henrikstranneheim]

@northwestwitch @moonso What is the status on this one? Do you need any more info from the raw data?

[northwestwitch]

@northwestwitch @moonso What is the status on this one? Do you need any more info from the raw data?

I'm not sure, I'll check!