A Variant Call Format reader for Python.
☆418Sep 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☆672Mar 20, 2026Updated last month
- annotate a VCF with other VCFs/BEDs/tabixed files☆401Aug 30, 2025Updated 7 months ago
- cython + htslib == fast VCF and BCF processing☆440Feb 23, 2026Updated 2 months ago
- 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…☆888Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Library for indexing VCF files for random access searches by rsID☆17Mar 2, 2026Updated last month
- A tool set for short variant discovery in genetic sequence data.☆205May 4, 2021Updated 4 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 6 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.☆554May 15, 2025Updated 11 months ago
- a lightweight db framework for exploring genetic variation.☆327Apr 28, 2020Updated 6 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆513Feb 26, 2026Updated 2 months ago
- ☆305Mar 9, 2026Updated last month
- Smart VCF parser DSL☆83May 24, 2022Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- VarDict☆203Jan 5, 2024Updated 2 years ago
- Efficient pythonic random access to fasta subsequences☆485Mar 19, 2026Updated last month
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated last week
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆58Mar 29, 2021Updated 5 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆342Feb 22, 2026Updated 2 months ago
- A Python package for exploring and analysing genetic variation data☆315Apr 1, 2026Updated 3 weeks ago
- This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file…☆131Feb 13, 2020Updated 6 years ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆865Apr 20, 2026Updated last week
- Tools to process and analyze deep sequencing data.☆759Jul 23, 2025Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,029Mar 11, 2025Updated last year
- Scalable gVCF merging and joint variant calling for population sequencing projects☆183Apr 12, 2024Updated 2 years ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,028Aug 24, 2024Updated last year
- A python tool for parsing pedigree files☆16Aug 29, 2017Updated 8 years ago
- Retrieve data in genomic intervals with a Python interface for tabix.☆82Aug 10, 2017Updated 8 years ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 11 months ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆330Mar 16, 2025Updated last year
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆195Apr 1, 2026Updated 3 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆846Apr 1, 2026Updated 3 weeks ago
- Plot structural variant signals from many BAMs and CRAMs☆566Jul 13, 2024Updated last year
- C library for high-throughput sequencing data formats☆918Apr 20, 2026Updated last week
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆545Apr 13, 2026Updated 2 weeks ago
- Count bases in BAM/CRAM files☆324Jan 31, 2022Updated 4 years ago
- Java utilities for Bioinformatics☆521Mar 25, 2026Updated last month
- Tools for working with SAM/BAM data☆610Dec 22, 2024Updated last year