Import Database

[J35P312]

Hello there!
I would like to import a SV database from another tool (such as SVDB or thousand genomes), and use it through loqusdb.

The databases are in vcf format. In the INFO column, there is a variant count tag, such a s OCC or AF.
Would it be possible to set the LoqusDB 'nr_events' tag based on that value?

//JEsper

[moonso]

This is a good idea. We need to look at some examples to get it to work...

[J35P312]

That would be great!
We have the SweGen database here:
https://swefreq.nbis.se/

There is also a thousand genomes SV database:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/

[J35P312]

This is solved using the import mongodb thingy right?

[moonso]

Not sure if it is the same thing... You would like to create a database from a VCF where counts are already added right? We could add that feature as well.