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☆682Mar 20, 2026Updated 4 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆406Jun 16, 2026Updated last month
- cython + htslib == fast VCF and BCF processing☆446Jun 25, 2026Updated 3 weeks 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…☆899Updated this week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Library for indexing VCF files for random access searches by rsID☆17Mar 2, 2026Updated 4 months ago
- A tool set for short variant discovery in genetic sequence data.☆206May 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 9 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.☆561May 15, 2025Updated last year
- a lightweight db framework for exploring genetic variation.☆329Apr 28, 2020Updated 6 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆527Updated this week
- ☆309Mar 9, 2026Updated 4 months ago
- VarDict☆204Jan 5, 2024Updated 2 years 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.
- Efficient pythonic random access to fasta subsequences☆488Mar 19, 2026Updated 4 months ago
- Smart VCF parser DSL☆83May 24, 2022Updated 4 years ago
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 3 months ago
- lumpy: a general probabilistic framework for structural variant discovery☆344Feb 22, 2026Updated 4 months ago
- A Python package for exploring and analysing genetic variation data☆317Jul 1, 2026Updated 2 weeks ago
- 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
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- 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☆1,041Jun 10, 2026Updated last month
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,029Aug 24, 2024Updated last year
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆196Jul 1, 2026Updated 2 weeks ago
- 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.☆82Aug 10, 2017Updated 8 years ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆330Mar 16, 2025Updated last year
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆565Updated this week
- Plot structural variant signals from many BAMs and CRAMs☆571Jul 13, 2024Updated 2 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Scalable gVCF merging and joint variant calling for population sequencing projects☆187Apr 12, 2024Updated 2 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆865May 2, 2026Updated 2 months ago
- C library for high-throughput sequencing data formats☆939Jul 9, 2026Updated last week
- A python tool for parsing pedigree files☆16Aug 29, 2017Updated 8 years ago
- Java utilities for Bioinformatics☆525Updated this week
- Count bases in BAM/CRAM files☆326Jul 10, 2026Updated last week
- Structural variant and indel caller for mapped sequencing data☆468Oct 11, 2025Updated 9 months ago