Workflows for Germline and Somatic Variant Calling

Automated variant calling pipelines for whole-exome sequencing (WES) data using GATK, DeepVariant, and other callers. Designed for large cohorts with best-practice quality filtering and annotation.

Overview

Snakemake workflows for reproducible genomic analyses of large cohort data designed to be executed on HPC. It makes use of conda environments for versioning of specific tools.

Pipelines

GATK HaplotypeCaller (Germline)

Traditional variant calling. Follows GATK Best Practices. File: GATK_HC_WES.smk

DeepVariant (Germline) in progress

Deep learning-based variant calling with GLnexus joint genotyping. Used for high-confidence consensus variants when paired with other callers. File: DeepVariant_WES.smk