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This Snakemake pipeline implements the GATK best-practices workflow
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling using GLnexus.