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

High performance data storage for importing, querying and transforming variants.

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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

Bioinformatics on GCP, AWS or Azure

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Whole Exome/Whole Genome Sequencing alignment pipeline

GitHub for the SIB courses NGS - Genome variant analysis

Sentieon DNAseq

Biopet docs

secondary analysis pipelines parallelized with apache spark

Nextflow implementation of the GATK HaplotypeCaller pipeline

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

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

Generates CWL files from the GATK documentation

Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.

Collecting Genotypes from ENA and make their SNPs

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.