hap.py
Haplotype VCF comparison tools (by Illumina)
TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
| hap.py | TileDB-VCF | |
|---|---|---|
| 2 | 4 | |
| 392 | 79 | |
| 1.0% | - | |
| 0.0 | 8.6 | |
| 5 months ago | 7 days ago | |
| C++ | C++ | |
| 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
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.
-
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 hap.py and TileDB-VCF you can also consider the following projects:
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
Hail - Cloud-native genomic dataframes and batch computing
GenomicSQLite - Genomics Extension for SQLite
gwas2vcf - Convert GWAS summary statistics to VCF
seq - A high-performance, Pythonic language for bioinformatics
truvari - Structural variant toolkit for VCFs
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings