truvari
Structural variant toolkit for VCFs (by ACEnglish)
cyvcf2
cython + htslib == fast VCF and BCF processing (by brentp)
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| truvari | cyvcf2 | |
|---|---|---|
| 1 | 1 | |
| 287 | 357 | |
| 5.6% | - | |
| 9.2 | 7.7 | |
| 2 days ago | about 2 months ago | |
| Python | Cython | |
| 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.
cyvcf2
Posts with mentions or reviews of cyvcf2.
We have used some of these posts to build our list of alternatives
and similar projects.
-
How can I index and query my VCF files by an INFO tag?
If you in command line, bcftools. If in python, https://github.com/brentp/cyvcf2
What are some alternatives?
When comparing truvari and cyvcf2 you can also consider the following projects:
Sniffles - Structural variation caller using third generation sequencing
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
gwas2vcf - Convert GWAS summary statistics to VCF
htslib - C library for high-throughput sequencing data formats
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
chatnoir-resiliparse - A robust web archive analytics toolkit
Hail - Cloud-native genomic dataframes and batch computing
hts.cr - HTSlib bindings for Crystal
locust - Write scalable load tests in plain Python 🚗💨
ruby-htslib - HTSlib bindings for Ruby