Segmented HAPlotype Estimation and Imputation Tool
☆96Dec 5, 2025Updated 3 months ago
Alternatives and similar repositories for shapeit5
Users that are interested in shapeit5 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Low Coverage Calling of Genotypes☆166Feb 28, 2026Updated 3 weeks ago
- Segmented HAPlotype Estimation and Imputation Tool☆98Aug 28, 2023Updated 2 years ago
- Phased structural variant discovery in pangenomes☆40Mar 14, 2026Updated last week
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 7 months ago
- Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions☆34Nov 14, 2024Updated last year
- ☆20Nov 30, 2023Updated 2 years ago
- Tools to work with GWAS-VCF summary statistics files☆130Feb 2, 2026Updated last month
- xSqueezeIt VCF/BCF Genotype data compressor with extensible compute friendly format☆14Aug 5, 2025Updated 7 months ago
- Pangenome-based genome inference☆162Dec 1, 2025Updated 3 months ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆32Jun 12, 2025Updated 9 months ago
- regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.☆256Nov 13, 2025Updated 4 months ago
- A module for improving the insertion sequences of structural variant calls☆33Jul 14, 2021Updated 4 years ago
- A bioinformatics pipeline to phase and impute genetic data☆29Updated this week
- linearize and simplify variation graphs using blocked partial order alignment☆61Feb 25, 2026Updated 3 weeks ago
- Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads☆82Jan 20, 2026Updated 2 months ago
- QUILT: Low coverage whole genome sequence imputation with large reference panels☆66Feb 11, 2026Updated last month
- dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCF…☆11Feb 3, 2021Updated 5 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆108Jun 6, 2021Updated 4 years ago
- ☆15Apr 2, 2024Updated last year
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- DNN-based small variant caller☆12May 2, 2022Updated 3 years ago
- A toolkit for exploring regions of variation in pangenomes☆14Feb 14, 2026Updated last month
- Annotation and Ranking of Structural Variation☆288Updated this week
- Kmer Analysis of Pileups for Genotyping☆37Mar 6, 2026Updated 2 weeks ago
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆17Mar 10, 2022Updated 4 years ago
- vcfdist: Accurately benchmarking phased variant calls☆85Feb 23, 2026Updated last month
- Deep learning framework for SV calling and genotyping☆113Nov 8, 2023Updated 2 years ago
- This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially …☆27Jul 28, 2025Updated 7 months ago
- Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis☆24Dec 15, 2025Updated 3 months ago
- SV detection tool for nanopore sequence reads☆97Mar 15, 2026Updated last week
- ☆13Mar 1, 2026Updated 3 weeks ago
- Population-scale genotyping using pangenome graphs☆197Jan 9, 2025Updated last year
- Fast, accurate and simple to use command line tool for variant detection in NGS data.☆12Sep 3, 2019Updated 6 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆179Apr 12, 2024Updated last year
- Genome Assembly Validation via Inter-SUNK distances in ONT reads☆15Feb 20, 2023Updated 3 years ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆54Mar 7, 2025Updated last year
- Phenome Exome Association and Correlation Of Key phenotypes☆35Aug 19, 2021Updated 4 years ago
- ☆30Mar 27, 2024Updated last year
- General purpose utility related to GAF files☆29Jan 27, 2026Updated last month