gatk

Official code repository for GATK versions 4 and up

This Snakemake pipeline implements the GATK best-practices workflow

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This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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

Learning the Variant Call Format

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Genomics using open source tools, running on GCP or AWS

Sentieon DNAseq

Biopet docs

Whole Exome/Whole Genome Sequencing alignment pipeline

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

🐍🔧 Snakemake wrappers for GATK.

Variant calling pipeline for germline enrichment NGS data

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

Variant calling + processing pipline using GATK based in Snakemake

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.

sysadmin tasks made easier

VAP : For Reference mapping and Variant detection.

Genome analysis pipeline that follows GATK best practices from Broad Institute

Toolbox for work with CloneHD application

Genome Analysis Toolkit

WDL-based pipelines

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

GATK and VARSCAN analysis pipeline