Comments (3)
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.
from gemini.
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 !
from gemini.
cutevariant looks nice!
from gemini.
Related Issues (20)
- add dict representation to GeminiRow HOT 4
- nogls-sub-bcolz.t43 test fails
- nogls.t2 test fails
- nogls-sub-bcolz.t14 test fails
- effstring.t03 test fails HOT 1
- cadd.t01 test fails
- Error in GEMINI Download
- Unexpected results when using OR with comp_hets HOT 4
- Documentation v30 HOT 1
- Error installing
- Wrong pysam version in Gemini 0.30.2 ('module' object has no attribute 'VariantRecord') HOT 1
- uninstall script
- on Galaxy platform: ValueError: processing failed on GEMINI chunk load
- Gemini load error with MuTect2 vcf 4.2
- facing traceback and 'syntax error' while running this code - gemini load --cores 3 -t snpEff -v $NORMVCF $db
- Failed fresh installation v0.30.2
- Gemini not found error while loading chunks from VCF HOT 4
- ValueError: Processing failed on GEMINI chunk load HOT 3
- Installation Error
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from gemini.