A Variant Call Format reader for Python.
☆419Sep 22, 2023Updated 2 years ago
Alternatives and similar repositories for PyVCF
Users that are interested in PyVCF are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Variant Call Format reader for Python.☆75Apr 19, 2015Updated 11 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆683Mar 20, 2026Updated 4 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆404Jun 16, 2026Updated last month
- cython + htslib == fast VCF and BCF processing☆446Jun 25, 2026Updated last month
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆904Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Library for indexing VCF files for random access searches by rsID☆17Mar 2, 2026Updated 5 months ago
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- commandline manipulation of genomic variants and NGS reads☆19Sep 6, 2024Updated last year
- Python 3 library with good support for both reading and writing VCF☆112Oct 2, 2025Updated 10 months ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆562May 15, 2025Updated last year
- a lightweight db framework for exploring genetic variation.☆328Apr 28, 2020Updated 6 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆528Updated this week
- ☆311Mar 9, 2026Updated 5 months ago
- Efficient pythonic random access to fasta subsequences☆489Mar 19, 2026Updated 4 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- VarDict☆204Jan 5, 2024Updated 2 years ago
- Smart VCF parser DSL☆83May 24, 2022Updated 4 years ago
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated 3 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated last year
- lumpy: a general probabilistic framework for structural variant discovery☆345Feb 22, 2026Updated 5 months ago
- A Python package for exploring and analysing genetic variation data☆317Aug 1, 2026Updated last week
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆58Mar 29, 2021Updated 5 years ago
- Tools to process and analyze deep sequencing data.☆762Updated this week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆876Apr 20, 2026Updated 3 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file…☆130Feb 13, 2020Updated 6 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,045Jun 10, 2026Updated 2 months ago
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆196Aug 1, 2026Updated last week
- C++ API & command-line toolkit for working with BAM data☆431May 18, 2025Updated last year
- Retrieve data in genomic intervals with a Python interface for tabix.