nf-core/sarek: a comprehensive & efficient somatic & germline variant calling workflow
Friederike Hanssen, Maxime U. Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Adam Talbot, Edmund Miller, Oskar Wacker, Nicholas Smith, Gisela Gabernet, and Sven Nahnsen
High-throughput, efficient, and reproducible pipelines are needed to ensure homogeneous data processing across different compute infrastructures with affordable resource usage.
We present nf-core/sarek 3.x, to explore single-nucleotide variants, structural variation, microsatellite instability, and copy-number alterations of germline, tumor-only, and tumor-normal pairs.
We will emphasize our efforts to reduce computational resource requirements including CRAM usage, replacing tools, and improving the scatter/gathering approach which ultimately lead to a reduction in cloud computing costs by 70%. In addition, we recently made efforts to include Sentieon for even faster processing as well as expanding nf-core/sarek with more tools to allow for post-variant calling and post-annotation processing.