This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
☆888Aug 28, 2026Updated this week
Alternatives and similar repositories for bcftools
Users that are interested in bcftools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,945Updated this week
- C library for high-throughput sequencing data formats☆946Updated this week
- 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
- bedtools - the swiss army knife for genome arithmetic☆1,045Jun 10, 2026Updated 2 months ago
- Official code repository for GATK versions 4 and up☆1,993Updated this week
- 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.
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,766Aug 7, 2026Updated 3 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆877Apr 20, 2026Updated 4 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆684Mar 20, 2026Updated 5 months ago
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,074Jul 31, 2026Updated 3 weeks ago
- PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a c…☆513Aug 18, 2026Updated last week
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,242May 19, 2026Updated 3 months ago
- The next version of bwa-mem☆858Oct 15, 2025Updated 10 months ago
- ☆312Mar 9, 2026Updated 5 months ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆568Updated this week
- 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.
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆871May 2, 2026Updated 3 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…☆907Aug 19, 2026Updated last week
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- Structural variation caller using third generation sequencing☆676Jul 20, 2026Updated last month
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,422Jul 30, 2026Updated last month
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated 4 months ago
- Structural variant and indel caller for mapped sequencing data☆468Oct 11, 2025Updated 10 months ago
- BEDOPS: high-performance genomic feature operations☆375Apr 29, 2025Updated last year
- 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.
- annotate a VCF with other VCFs/BEDs/tabixed files☆404Jun 16, 2026Updated 2 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆534Updated this week
- cython + htslib == fast VCF and BCF processing☆446Jun 25, 2026Updated 2 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆757Aug 6, 2026Updated 3 weeks ago
- tools for working with genome variation graphs☆1,334Updated this week
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆711Updated this week
- Toolkit for processing sequences in FASTA/Q formats☆1,559Jun 1, 2025Updated last year
- lumpy: a general probabilistic framework for structural variant discovery☆346Feb 22, 2026Updated 6 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆338May 27, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Haplotype VCF comparison tools☆471Dec 7, 2023Updated 2 years ago
- Note: tabix and bgzip binaries are now part of the HTSlib project.☆92Aug 3, 2021Updated 5 years ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆283Jul 7, 2026Updated last month
- A quality control analysis tool for high throughput sequencing data☆614Jul 20, 2026Updated last month
- A fast and sensitive gapped read aligner☆811Jun 1, 2026Updated 2 months ago
- Transcript assembly and quantification for RNA-Seq☆529Aug 9, 2026Updated 2 weeks ago
- VCF-kit: Assorted utilities for the variant call format☆136May 22, 2026Updated 3 months ago