gwas2vcf
Convert GWAS summary statistics to VCF (by MRCIEU)
TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
| gwas2vcf | TileDB-VCF | |
|---|---|---|
| 1 | 4 | |
| 39 | 80 | |
| - | - | |
| 0.0 | 8.6 | |
| about 1 year ago | 5 days ago | |
| Python | C++ | |
| 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.
gwas2vcf
Posts with mentions or reviews of gwas2vcf.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-09-01.
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Nuitka: An extremely compatible Python compiler
Here is the original repo I have tried to speed up using:
python -m nuitka --clang --follow-imports main.py
repo: https://github.com/MRCIEU/gwas2vcf
If someone can make the program run faster by whatever means, it will make a bunch of people quite happy.
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
What are some alternatives?
When comparing gwas2vcf and TileDB-VCF you can also consider the following projects:
truvari - Structural variant toolkit for VCFs
Hail - Cloud-native genomic dataframes and batch computing
graalvm-ten-things - Top 10 Things To Do With GraalVM
pybenchmarks - Python Interpreters Benchmarks
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
TileDB - The Universal Storage Engine
py2many - Transpiler of Python to many other languages
gw - Genome browser and variant annotation