cython + htslib == fast VCF and BCF processing
☆430Feb 23, 2026Updated last week
Alternatives and similar repositories for cyvcf2
Users that are interested in cyvcf2 are comparing it to the libraries listed below
Sorting:
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 5 months ago
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆304Nov 14, 2025Updated 3 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆146Feb 17, 2026Updated 2 weeks ago
- Structural variant toolkit for VCFs☆397Jan 23, 2026Updated last month
- Plot structural variant signals from many BAMs and CRAMs☆560Jul 13, 2024Updated last year
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆826Feb 10, 2026Updated 3 weeks ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 2 weeks ago
- A Python package for exploring and analysing genetic variation data☆315Feb 1, 2026Updated last month
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- Haplotype VCF comparison tools☆458Dec 7, 2023Updated 2 years ago
- genetic variant expressions, annotation, and filtering for great good.☆273Dec 15, 2025Updated 2 months ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆669Oct 31, 2025Updated 4 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…☆882Feb 2, 2026Updated last month
- The D4 Quantitative Data Format☆169Nov 28, 2025Updated 3 months ago
- Efficient pythonic random access to fasta subsequences☆482Sep 3, 2025Updated 6 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆132Oct 14, 2025Updated 4 months ago
- nim wrapper for htslib for parsing genomics data files☆157Dec 15, 2025Updated 2 months ago
- Cloud-native genomic dataframes and batch computing☆1,050Updated this week
- Performant Pythonic GenomicRanges☆494Jan 27, 2026Updated last month
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 8 months ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- Population-scale genotyping using pangenome graphs☆196Jan 9, 2025Updated last year
- lumpy: a general probabilistic framework for structural variant discovery☆338Feb 22, 2026Updated last week
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆106Jun 6, 2021Updated 4 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆176Apr 12, 2024Updated last year
- Scalable genetics toolkit☆274Sep 30, 2025Updated 5 months ago
- create a gemini-compatible database from a VCF☆55Jan 5, 2021Updated 5 years ago
- Per-base per-nucleotide depth analysis☆146Feb 4, 2026Updated last month
- tools for working with genome variation graphs☆1,300Updated this week
- a lightweight db framework for exploring genetic variation.☆326Apr 28, 2020Updated 5 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆334May 27, 2025Updated 9 months ago
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆398Feb 3, 2026Updated last month
- BAM Statistics, Feature Counting and Annotation☆152Updated this week
- Structural variation and indel detection by local assembly☆252Sep 16, 2025Updated 5 months ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆328Mar 16, 2025Updated 11 months ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 2 years ago