hap.py
Haplotype VCF comparison tools (by Illumina)
truvari
Structural variant toolkit for VCFs (by ACEnglish)
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| hap.py | truvari | |
|---|---|---|
| 2 | 1 | |
| 392 | 287 | |
| 2.6% | 5.6% | |
| 0.0 | 9.2 | |
| 5 months ago | 3 days ago | |
| C++ | Python | |
| GNU General Public License v3.0 or later | 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.
hap.py
Posts with mentions or reviews of hap.py.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Help running hap.py
I have been tasked with benchmarking a variant calling pipeline running hap.py as part of my bioinformatics MSc project.
- cream π
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 hap.py and truvari you can also consider the following projects:
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
Sniffles - Structural variation caller using third generation sequencing
GenomicSQLite - Genomics Extension for SQLite
gwas2vcf - Convert GWAS summary statistics to VCF
seq - A high-performance, Pythonic language for bioinformatics
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
gw - Genome browser and variant annotation
cyvcf2 - cython + htslib == fast VCF and BCF processing
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Hail - Cloud-native genomic dataframes and batch computing
locust - Write scalable load tests in plain Python 🚗💨