gatk-workflows / gatk4-somatic-snvs-indelsView external linksLinks
This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
☆78Mar 9, 2020Updated 5 years ago
Alternatives and similar repositories for gatk4-somatic-snvs-indels
Users that are interested in gatk4-somatic-snvs-indels are comparing it to the libraries listed below
Sorting:
- This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organi…☆44Mar 10, 2020Updated 5 years ago
- ☆69Jun 21, 2022Updated 3 years ago
- Workflows for germline short variant discovery with GATK4☆139May 7, 2021Updated 4 years ago
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆160Aug 10, 2022Updated 3 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Jan 24, 2020Updated 6 years ago
- Detect and visualize microsatellite instability(MSI) from NGS data☆32Jun 4, 2019Updated 6 years ago
- This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are a…☆22Mar 9, 2020Updated 5 years ago
- Repository☆10Oct 23, 2024Updated last year
- ☆444Jun 15, 2020Updated 5 years ago
- Westlake BioBank for Chinese pilot project☆10May 17, 2023Updated 2 years ago
- 肿瘤突变负荷学习笔记（tumor mutation burden）☆16Dec 10, 2019Updated 6 years ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆57Mar 29, 2021Updated 4 years ago
- Deduplication for cfDNA sequencing data☆11Jul 5, 2017Updated 8 years ago
- ☆36Mar 16, 2021Updated 4 years ago
- amplicon/smMIP mapping and analysis pipeline☆11Dec 8, 2022Updated 3 years ago
- This is the repository which contains the code that was used to generate the results and figures of the “Single-cell RNA-sequencing revea…☆12Jun 21, 2024Updated last year
- Simple script to generate whole-genome coverage plots☆19Jun 23, 2015Updated 10 years ago
- Gene fusion detection and visualization☆131Feb 21, 2022Updated 3 years ago
- Data Visualizations for the #30DayChartChallenge☆11Apr 15, 2024Updated last year
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated last year
- ☆10Feb 25, 2024Updated last year
- Use gene expression to predict phenotype sample information☆19Feb 13, 2018Updated 8 years ago
- Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; a…☆71Feb 6, 2026Updated last week
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Sep 28, 2022Updated 3 years ago
- Multiplex Primer Design☆12May 3, 2020Updated 5 years ago
- GWAS analysis process based on EMMAX software☆18Dec 12, 2023Updated 2 years ago
- ☆12Feb 19, 2021Updated 4 years ago
- GWAS SNP Regulatory Analysis Tool☆17Mar 19, 2015Updated 10 years ago
- UVC, a very accurate small-variant caller (https://doi.org/10.1093/bib/bbab458)☆14May 18, 2025Updated 8 months ago
- VarDict☆201Jan 5, 2024Updated 2 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆55Oct 29, 2020Updated 5 years ago
- predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data☆27Sep 13, 2023Updated 2 years ago
- A bioinformatics tool for SV detection and virus integration discovery☆21Sep 12, 2017Updated 8 years ago
- A fast lossless FASTQ compressor with ultra-high compression ratio☆143May 28, 2025Updated 8 months ago
- STAR-Fusion codebase☆248Oct 4, 2025Updated 4 months ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆57Mar 19, 2020Updated 5 years ago
- Gene Fusion Visualiser☆51Jan 15, 2023Updated 3 years ago
- Set of script for the paper on the cattle graph genome☆13Jan 10, 2023Updated 3 years ago
- Generate duplex/single consensus reads to reduce sequencing noises and remove duplications☆126Oct 27, 2023Updated 2 years ago