Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
☆213Mar 19, 2021Updated 5 years ago
Alternatives and similar repositories for benchmarking-tools
Users that are interested in benchmarking-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Haplotype VCF comparison tools☆475Dec 7, 2023Updated 2 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆339May 27, 2025Updated last year
- This repository contains data indexes from NIST's Genome in a Bottle project.☆275Nov 30, 2023Updated 2 years ago
- Bayesian haplotype-based mutation calling☆326Feb 13, 2026Updated 8 months ago
- Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls☆46Jan 26, 2022Updated 4 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- The Platinum Genomes Truthset☆90Nov 8, 2017Updated 8 years ago
- Structural variant toolkit for VCFs☆428Oct 3, 2026Updated last month
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆687Oct 2, 2026Updated last month
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 6 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆404Jun 16, 2026Updated 4 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆153Feb 17, 2026Updated 8 months ago
- tools for adding mutations to existing .bam files, used for testing mutation callers☆253Aug 5, 2026Updated 2 months ago
- ☆55Jun 24, 2020Updated 6 years ago
- Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium…☆85Nov 16, 2022Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Workflows for germline short variant discovery with GATK4☆145May 7, 2021Updated 5 years ago
- vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph re…☆42Sep 16, 2021Updated 5 years ago
- Toolset for SV simulation, comparison and filtering☆426Dec 1, 2023Updated 2 years ago
- VarDict☆204Jan 5, 2024Updated 2 years ago
- The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data☆32Feb 20, 2018Updated 8 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆879Updated this week
- reference implementation of GA4GH WGS Quality Control Standards☆12Oct 20, 2026Updated last week
- What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.☆38Sep 13, 2023Updated 3 years ago
- Tools for working with genomic and high throughput sequencing data.☆379Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- This repository contains information about latest release from Genome in a Bottle project☆75Aug 30, 2019Updated 7 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆120Jun 6, 2021Updated 5 years ago
- Structural variant and indel caller for mapped sequencing data☆467Oct 11, 2025Updated last year
- GA4GH Quality Control of Whole Genome Sequencing's metrics definition, benchmark resources and reference implementations☆26Updated this week
- tools for working with genome variation graphs☆1,348Updated this week
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆341Oct 23, 2026Updated last week
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,031Aug 24, 2024Updated 2 years ago
- Official code repository for GATK versions 4 and up☆2,009Updated this week
- Plot structural variant signals from many BAMs and CRAMs☆573Jul 13, 2024Updated 2 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.
- VCF visualization interface☆184Updated this week
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- Code used to generate manuscript figures and results.☆14Jan 10, 2024Updated 2 years ago
- a lightweight db framework for exploring genetic variation.☆327Apr 28, 2020Updated 6 years ago
- A tool for estimating repeat sizes☆219Jan 30, 2024Updated 2 years ago
- Read-based phasing of genomic variants, also called haplotype assembly☆433Oct 9, 2026Updated 3 weeks ago
- R tools to interact with hap.py output☆16Jul 12, 2019Updated 7 years ago