Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline
☆59Mar 19, 2020Updated 6 years ago
Alternatives and similar repositories for broad-prod-wgs-germline-snps-indels
Users that are interested in broad-prod-wgs-germline-snps-indels are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Workflows for germline short variant discovery with GATK4☆145May 7, 2021Updated 5 years ago
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆162Aug 10, 2022Updated 4 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
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆56Oct 29, 2020Updated 6 years ago
- A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.☆13Feb 23, 2021Updated 5 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- seqpac - A Framework for small RNA analysis in R using Sequence-Based Counts☆10Oct 12, 2026Updated 3 weeks ago
- Work supporting the comparison of SnpEff and VEP effect prediction and HGVS identifiers☆11Mar 15, 2017Updated 9 years ago
- Workflows for converting between sequence data formats☆40Sep 5, 2021Updated 5 years ago
- Deduplication for cfDNA sequencing data☆11Jul 5, 2017Updated 9 years ago
- barcode demultiplexing☆22Jun 4, 2019Updated 7 years ago
- Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the …☆28Jan 4, 2021Updated 5 years ago
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 6 months ago
- Sync paired-end FASTA/Q files and keep singleton reads☆19Aug 29, 2026Updated 2 months ago
- Annotation of VCF variants with functional impact and from databases (executable+library)☆69Updated this week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools☆54Dec 19, 2019Updated 6 years ago
- an R package for ancestry analysis☆37Jan 9, 2019Updated 7 years ago
- VIPER (Variant InsPector and Expert Rating tool) can be utilised to view variant calls and decide whether or not those are true or false …☆16Jan 17, 2022Updated 4 years ago
- Concordance and contamination estimator for tumor–normal pairs☆60Oct 22, 2024Updated 2 years ago
- Please consider using/contributing to https://github.com/nf-core/sarek☆18Jan 3, 2019Updated 7 years ago
- a lightweight db framework for exploring genetic variation.☆327Apr 28, 2020Updated 6 years ago
- Official code repository for GATK versions 4 and up☆2,009Updated this week
- Genomes on the Cloud, Mapping & Variant Calling Pipelines☆33Mar 24, 2017Updated 9 years ago
- Variant caller GUI + genetic disease analysis☆22Apr 29, 2020Updated 6 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- gnomAD browser pre-ASHG 2018☆32Nov 2, 2020Updated 6 years ago
- Genetic Relationship And Fingerprinting☆14Feb 6, 2023Updated 3 years ago
- variant integration methods for the 1000 Genomes Project☆21Jan 16, 2018Updated 8 years ago
- Survival Analysis for Protein-Level TCGA Analysis☆12Nov 30, 2018Updated 7 years ago
- A small repo for storing the code for making the files and html for CCRs.☆22Oct 22, 2019Updated 7 years ago
- ☆18Nov 15, 2021Updated 4 years ago
- Generate duplex/single consensus reads to reduce sequencing noises and remove duplications☆127Oct 27, 2023Updated 3 years ago
- Quality control pipeline for human exome/genome cohorts☆10Oct 23, 2026Updated last week
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆98Apr 20, 2026Updated 6 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Probabilistic HLA typing☆35Aug 31, 2019Updated 7 years ago
- Tools for doing x way meta-analysis☆12Apr 12, 2022Updated 4 years ago
- GWAS SNP Regulatory Analysis Tool☆17Mar 19, 2015Updated 11 years ago
- FastSMC is a method to quickly and accurately estimate pairwise identical-by-descent (IBD) regions in the genome. FastSMC estimates the a…☆15Sep 2, 2021Updated 5 years ago
- 肿瘤突变负荷学习笔记(tumor mutation burden)☆17Dec 10, 2019Updated 6 years ago
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆236Feb 17, 2022Updated 4 years ago
- Liftover VCF files☆19Dec 10, 2016Updated 9 years ago