TileDB-VCF
gw
| TileDB-VCF | gw | |
|---|---|---|
| 4 | 2 | |
| 80 | 132 | |
| - | - | |
| 8.6 | 9.5 | |
| 3 days ago | 6 days ago | |
| C++ | C++ | |
| MIT License | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
TileDB-VCF
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Has anyone stored/queried VCFs and their variant records in a relational database?
Perhaps of interest https://github.com/TileDB-Inc/TileDB-VCF
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[TileDB webinar] Population genomics is a data management problem
Here are the docs to the open-source TileDB-VCF storage engine: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics
gw
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Bam file genome viewing and whole chromosome plotting on a phone
https://github.com/kcleal/gw/wiki/GW-on-Android if you still want to try
What are some alternatives?
Hail - Cloud-native genomic dataframes and batch computing
constraints - Tools for programming with ConstraintKinds in GHC
gwas2vcf - Convert GWAS summary statistics to VCF
scat - Password scatterer. Eliminates password reuse by generating deterministically unique passwords for each service (website, email address, etc.), all from a single password.
truvari - Structural variant toolkit for VCFs
deeplabel - A cross-platform desktop image annotation tool for machine learning
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
sbv - SMT Based Verification in Haskell. Express properties about Haskell programs and automatically prove them using SMT solvers.
TileDB - The Universal Storage Engine
hap.py - Haplotype VCF comparison tools
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
yolo_annotation_tool - Annotation tool for YOLO in opencv