gatk

Official code repository for GATK versions 4 and up

This Snakemake pipeline implements the GATK best-practices workflow

Learning the Variant Call Format

GATK RNA-Seq Variant Calling in Nextflow

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure

Whole Exome/Whole Genome Sequencing alignment pipeline

Sentieon DNAseq

Biopet docs

Nextflow implementation of the GATK pipeline

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

Generates CWL files from the GATK documentation

Collecting Genotypes from ENA and make their SNPs

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Variant calling pipeline for germline enrichment NGS data

🐍🔧 Snakemake wrappers for GATK.

Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.

secondary analysis pipelines parallelized with apache spark

An Efficient Design of a Next Generation Sequencing pipeline with Apache Spark

Genome analysis pipeline that follows GATK best practices from Broad Institute

VAP : For Reference mapping and Variant detection.

Variant calling + processing pipline using GATK based in Snakemake

sysadmin tasks made easier

msgen: R functions for interfacing with the Microsoft Genomics service on Azure.

Genome Analysis Toolkit

WDL-based pipelines

Toolbox for work with CloneHD application

Bash and Python pipelines and scripts from the Invertebrates & Microbiology Group at the Queensland University of Technology to help make data analysis easy.