TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
truvari
Structural variant toolkit for VCFs (by ACEnglish)
| TileDB-VCF | truvari | |
|---|---|---|
| 4 | 1 | |
| 80 | 291 | |
| - | 2.1% | |
| 8.6 | 9.2 | |
| 3 days ago | 9 days ago | |
| C++ | Python | |
| MIT License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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
Posts with mentions or reviews of TileDB-VCF.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-12.
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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
truvari
Posts with mentions or reviews of truvari.
We have used some of these posts to build our list of alternatives
and similar projects.
-
VCF files for ML and AI
If you use python and are familiar with pandas (which is more data science friendly than anything VCF), Truvari has a utility for conversion. `truvari vcf2df input.vcf.gz output.jl` If the VCFs are very large, I'd also consider scikit-allele.
What are some alternatives?
When comparing TileDB-VCF and truvari you can also consider the following projects:
Hail - Cloud-native genomic dataframes and batch computing
Sniffles - Structural variation caller using third generation sequencing
gwas2vcf - Convert GWAS summary statistics to VCF
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
cyvcf2 - cython + htslib == fast VCF and BCF processing
TileDB - The Universal Storage Engine
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
locust - Write scalable load tests in plain Python 🚗💨
gw - Genome browser and variant annotation
hap.py - Haplotype VCF comparison tools