Clinical Whole Genome and Exome Sequencing Pipeline

Whole Exome/Whole Genome Sequencing alignment pipeline

Workflows for germline short variant discovery with GATK4

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

Official code repository for GATK versions 4 and up

A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framework in Python.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

This Snakemake pipeline implements the GATK best-practices workflow