TY - JOUR T1 - Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants JF - bioRxiv DO - 10.1101/316976 SP - 316976 AU - Maxime Garcia AU - Szilveszter Juhos AU - Malin Larsson AU - Pall I. Olason AU - Marcel Martin AU - Jesper Eisfeldt AU - Sebastian DiLorenzo AU - Johanna Sandgren AU - Teresita Diaz de Ståhl AU - Valtteri Wirta AU - Monica Nistér AU - Björn Nystedt AU - Max Käller Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/05/09/316976.abstract N2 - Summary Whole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.Availability Source code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project. ER -