Show local variant archive date also on SV pages

[dnil]

The little hover over local observations archive only shows the date on SNV pages. 😅

[dnil]

Ah, ok, the info actually not in the SV VCF. Perhaps it will be after the new dump, @jemten?

To show this, we expect one of the following in the variant VCF:

A Date string on the loqusdb software:

##Software=<ID=loqusdb,Version=2.5,Date="2020-08-21 09:02",CommandLineOptions="">

This appears missing from both SNV and SV files.

Or an obs INFO tag, showing the dated source of the dump in Description:

##INFO=<ID=Obs,Number=1,Type=Integer,Description="The number of observations for the variant (from /home/proj/production/rare-disease/references/references_11.0/grch37_loqusdb_snv_indel_variants_export-20220905-.vcf.gz)">

This is ok in the SNV VCF, but for the SV VCFs we have less informative Descriptions like

##INFO=<ID=clinical_genomics_loqusObs,Number=1,Type=Integer,Description="The number of occurances of the event in the database">

[dnil]

I suspect the latter may resolve with a new dump - I dont find that string in later versions of loqusdb? 😊

[jemten]

We would need to update MIP for this to happen as we right now don't transfer the loqusdb header string to the annotated vcf. We can see about making a patch after the release of MIP 12.0.0

[dnil]

Ah it's only transferred to the SNV version? It's ok there..

[jemten]

To me, this string ##Software=<ID=loqusdb,Version=2.5,Date="2020-08-21 09:02",CommandLineOptions=""> looks to be missing in both snv and SV. That string comes from the loqus vcf.
For SNVs we annotate with vcfanno which will add the filename of the source file. This filename contains the date of the loqus dump. For SVs we annotate with SVDB and the filename of the source annotation isn't added to the header. Would require some light tweaking to get this consistent.

[dnil]

Had a ping on this today. Not saying it must happen, but it would be used some at least. Do we have it well annotated with raredisease e.g.?

[jemten]

Thanks for pinging @dnil,
We could add the file name to the TAG description in a similar way as is done by vcfanno for the SNVs by adding the filename here.
https://github.com/J35P312/SVDB/blob/3e95936b13dda6507d4f9648824727068b4174ea/svdb/query_module.py#L31
Since it won't be fixed in MIP I'm transferring the issue to raredisease

[jemten]

Started some work on a svdb "fix" to add the database path to the header. Would look like this:

##INFO=<ID=clinical_genomics_loqusObs,Number=1,Type=Integer,Description="The number of occurrences of the event in the database /home/proj/production/rare-disease/references/references_12.0/grch37_loqusdb_sv_variants_export-20250611-.vcf">
##INFO=<ID=clinical_genomics_loqusFrq,Number=1,Type=Float,Description="The frequency of the event in the database /home/proj/production/rare-disease/references/references_12.0/grch37_loqusdb_sv_variants_export-20250611-.vcf">

What do you think @dnil, would it solve the issue for scout?

[dnil]

I think we could make that work: the parsing for Description is currently probably only triggered for observation counts named exactly "Obs", but extending that to "*Obs" seems very natural!