truvari
Structural variant toolkit for VCFs (by ACEnglish)
gwas2vcf
Convert GWAS summary statistics to VCF (by MRCIEU)
Our great sponsors
| truvari | gwas2vcf | |
|---|---|---|
| 1 | 1 | |
| 287 | 39 | |
| 5.6% | - | |
| 9.2 | 0.0 | |
| 2 days ago | about 1 year ago | |
| Python | 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.
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.
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.
-
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.
What are some alternatives?
When comparing truvari and gwas2vcf you can also consider the following projects:
Sniffles - Structural variation caller using third generation sequencing
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
graalvm-ten-things - Top 10 Things To Do With GraalVM
cyvcf2 - cython + htslib == fast VCF and BCF processing
pybenchmarks - Python Interpreters Benchmarks
Hail - Cloud-native genomic dataframes and batch computing
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
locust - Write scalable load tests in plain Python 🚗💨