question regarding sqlite Blob

[dridk]

Hi,

I see you store sample data ( like genotype ) as blob into sqlite database. I am really curious how do you query this fields in raw sql ? for instance, how to get variant where sample boby is heterozygous ?

[brentp]

Hi, we have to decode the blob to do any queries on genotypes so it's not very efficient. If you use vcf2db.py there is an option to put the genotypes into a separate table that can be indexed. We recommend to use slivar instead of gemini unless you have specific use for gemini.

[dridk]

Thanks ! I m creating my own GUI application based on sqlite like you. So, I am investigating how other project is doing : You can have a look here! https://github.com/labsquare/cutevariant

Thanks ! I didn't know slivar !

[brentp]

cutevariant looks nice!