I’m standing up a production bioinformatics pipeline that’ll be producing standard VCF files. I’d like to store this data in an SQL database that ingest the VCFs and allow me and my team to easily query and visualize many VCFs. Because multiple people will have access to the data, roles/permissions need to be built in. I don’t want to create this system from scratch, but it needs to be both robust and intuitive. Are there any products like this available today?

[Edit]: The answers provided to this question are on the right track, but only provide a small slice of the functionality I'm looking for. For starters, I'm looking for a hosted/managed solution; something potentially like Basespace, but more user-friendly and not quite so bloated.

Additionally, the linked solutions are mostly about getting vcfs into a db, but don't make much headway into providing exploration/visualization tooling.

  • $\begingroup$ May be something useful here bioinformatics.stackexchange.com/questions/15248/… $\endgroup$
    – user438383
    Aug 23, 2022 at 7:44
  • $\begingroup$ Hi @JessimeKirk IMO it is better to ask a question focussed on a single specific issue in most cases. Maybe summarise the answer kindly provided above and focus on a Basespace type solution? $\endgroup$
    – M__
    Aug 25, 2022 at 2:30
  • $\begingroup$ If you are open to non-free solutions, check out VarSome Clinical. (disclaimer: I work for the company behind this, so I am obviously not impartial, but it really is good, honest!). $\endgroup$
    – terdon
    Aug 25, 2022 at 12:32
  • $\begingroup$ Like terdon says, you may have to go for commercial solutions if you want layman storage/visualization for VCF files. You're looking to offload bioinformatics work and no free tool can effectively replace something a human being needs to do $\endgroup$
    – Ram RS
    Aug 25, 2022 at 14:59


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