gwas2vcf VS truvari

Compare gwas2vcf vs truvari and see what are their differences.

gwas2vcf

Convert GWAS summary statistics to VCF (by MRCIEU)
Gwas Bioinformatics Vcf Converter summary-statistics
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truvari

Structural variant toolkit for VCFs (by ACEnglish)
structural-variation Vcf Bioinformatics Data Science Genomics vcf-comparison annotation-tool benchmark-scripts sequencing-data sv-merging
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gwas2vcf truvari
1 1
39 291
- 3.4%
0.0 9.2
about 1 year ago 11 days 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.
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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
    10 projects | news.ycombinator.com | 1 Sep 2021
    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.

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
    1 project | /r/bioinformatics | 12 Nov 2021
    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 gwas2vcf and truvari you can also consider the following projects:

TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.

Sniffles - Structural variation caller using third generation sequencing

graalvm-ten-things - Top 10 Things To Do With GraalVM

pybenchmarks - Python Interpreters Benchmarks

cyvcf2 - cython + htslib == fast VCF and BCF processing

sgkit - We've moved to https://github.com/sgkit-dev/sgkit

Hail - Cloud-native genomic dataframes and batch computing

locust - Write scalable load tests in plain Python 🚗💨

py2many - Transpiler of Python to many other languages

hap.py - Haplotype VCF comparison tools

gwas2vcf vs TileDB-VCF truvari vs Sniffles gwas2vcf vs graalvm-ten-things truvari vs TileDB-VCF gwas2vcf vs pybenchmarks truvari vs cyvcf2 gwas2vcf vs sgkit truvari vs Hail gwas2vcf vs Hail truvari vs locust gwas2vcf vs py2many truvari vs hap.py