PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive update to it.
☆487Mar 1, 2026Updated last week
Alternatives and similar repositories for plink-ng
Users that are interested in plink-ng are comparing it to the libraries listed below
Sorting:
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆846Updated this week
- LD Score Regression (LDSC)☆763Jan 16, 2026Updated last month
- Eigen tools by Nick Patterson and Alkes Price lab☆199Nov 3, 2023Updated 2 years ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆551May 15, 2025Updated 9 months ago
- Ultrafast GPU-enabled QTL mapper☆206Jun 29, 2025Updated 8 months ago
- A tool to build a website to browse hundreds or thousands of GWAS.☆192Sep 11, 2025Updated 5 months ago
- A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores☆202Aug 21, 2024Updated last year
- Flexible genotype query among 30,000+ samples whole-genome☆94Sep 4, 2019Updated 6 years ago
- Low Coverage Calling of Genotypes☆166Feb 28, 2026Updated last week
- Rare variant test software for next generation sequencing data☆141Jan 26, 2022Updated 4 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆669Oct 31, 2025Updated 4 months ago
- A variational framework for inferring population structure from SNP genotype data.☆143Jan 6, 2023Updated 3 years ago
- ☆196May 2, 2022Updated 3 years ago
- Cloud-native genomic dataframes and batch computing☆1,050Updated this week
- ☆103Jun 26, 2022Updated 3 years ago
- Segmented HAPlotype Estimation and Imputation Tool☆98Aug 28, 2023Updated 2 years ago
- regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.☆255Nov 13, 2025Updated 3 months ago
- A comprehensive tutorial about GWAS and PRS☆970Apr 1, 2023Updated 2 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆106Jun 6, 2021Updated 4 years ago
- A genotype query interface.☆136Mar 29, 2021Updated 4 years ago
- Population-scale genotyping using pangenome graphs☆196Jan 9, 2025Updated last year
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,053Feb 4, 2026Updated last month
- Codebook from my GWAS cookbook☆193May 26, 2022Updated 3 years ago
- ☆69Updated this week
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.☆165May 9, 2025Updated 10 months ago
- Graph realignment tools for structural variants☆166Dec 8, 2022Updated 3 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,025Mar 11, 2025Updated 11 months ago
- C library for high-throughput sequencing data formats☆910Updated this week
- R package for the analysis of massive SNP arrays.☆219Aug 21, 2025Updated 6 months ago
- MOsaic CHromosomal Alterations (MoChA) caller☆92Aug 22, 2025Updated 6 months ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆177Apr 12, 2024Updated last year
- tools for working with genome variation graphs☆1,300Mar 2, 2026Updated last week
- Read-based phasing of genomic variants, also called haplotype assembly☆409Dec 31, 2025Updated 2 months ago
- GCTA software☆106Jul 9, 2025Updated 8 months ago
- Structural variant toolkit for VCFs☆397Updated this week
- ☆101Apr 22, 2024Updated last year
- Jasmine: SV Merging Across Samples☆242Dec 20, 2024Updated last year
- 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