<section data-background-image="https://maxulysse.github.io/assets/img/background/Sarek-Park-02.jpg" data-background-opacity=0.5 > # Sarek ## a workflow to detect germline and somatic mutations in WGS/WES Maxime Garcia <small> [<i class="fab fa-twitter"></i> @gau](https://twitter.com/gau) [<i class="fab fa-github"></i> @MaxUlysse](https://github.com/MaxUlysse) [<i class="fa fa-globe-europe"></i> maxulysse.github.io](https://maxulysse.github.io/) </small> 4th Scandinavian Seminar on Translational Pathology <small> Solstrand, Bergen - 2019/10/24 </small> --- [](https://ki.se/forskning/barntumorbanken) <!-- .element class="image-H10" --> Swedish Childhood Tumor Biobank --- [](https://scilifelab.se/) <!-- .element class="image-H10" --> National centre for molecular biosciences with focus on health and environmental research [](https://ki.se/) <!-- .element class="image-H75" --> | [](https://www.kth.se/) <!-- .element class="image-H75" --> | [](https://www.su.se/) <!-- .element class="image-H75" --> | [](https://www.uu.se/) <!-- .element class="image-H75" --> :-:|:-:|:-:|:-: Note: * SciLifeLab is several infrastructures === [](https://ngisweden.scilifelab.se/) <!-- .element class="image-H10" --> * State-of-the-art infrastructure * Sequencing (DNA, RNA ...) * Guidelines and support * Sample collection, study design, protocol selection * Bioinformatics analysis === [](https://www.nbis.se/) <!-- .element class="image-H10" --> * Swedish ELIXIR node * Bioinformatics support for Swedish researchers --- ## What is Sarek <div class="fragment fade-in" data-fragment-index="2"> A [National Park](https://www.sverigesnationalparker.se/en/choose-park---list/sarek-national-park/) in Northern Sweden. <small> * Long, deep, narrow valleys and wild, turbulent water * A tortuous delta landscape * Completely lacking in comfortable accommodations * One of Sweden’s most inaccessible national parks * There are no roads leading up to the national park </small> </div> --- <section data-background-image="https://maxulysse.github.io/assets/img/background/Sarek-Park-02.jpg"> --- [](https://nf-co.re/sarek) <!-- .element class="image-H10" --> <div class="fragment fade-in" data-fragment-index="2"> * Open-Source Nextflow Pipeline * Developed at NGI * In collaboration with NBIS * Support from Barntumörbanken </div> === [](https://www.nextflow.io/) <!-- .element class="image-50" --> <div class="fragment fade-in" data-fragment-index="2"> * Workflow manager * Data driven language * Portable (executable on multiple platforms) * Shareable and reproducible (with containers) </div> === ## Software dependencies [](https://bioconda.github.io/) <!-- .element class="image-H75" --> | [](https://www.docker.com/) <!-- .element class="image-H75" --> | [](https://sylabs.io/singularity/) <!-- .element class="image-H75" --> :-:|:-:|:-: <div class="fragment fade-in" data-fragment-index="2"> * All tools are installed with Bioconda, which allow set up of a new environment * Bundled into a Docker container, which Nextflow can automatically download from DockerHub * Built from the Docker container, Singularity images can solve HPC container problems </div> === ## Reference genomes [AWS iGenomes](https://registry.opendata.aws/aws-igenomes/) * GRCh37 * GRCh38 --- ## Multiple flavors  <!-- .element class="image-10" --> <div class="fragment fade-in" data-fragment-index="2">  <!-- .element class="image-10" --> |  <!-- .element class="image-10" --> :-:|:-: </div> === ## WES and Targeted Sequencing  <!-- .element class="image-25" --> --- ## Preprocessing [](https://software.broadinstitute.org/gatk/best-practices/) <!-- .element class="image-H25" --> Based on GATK Best Practices (GATK 4.1.2.0) <div class="fragment fade-in" data-fragment-index="2"> * Reads mapped to reference genome with `bwa` * Duplicates marked with `picard MarkDuplicates` * Recalibrate with `GATK BaseRecalibrator` </div> === ## Germline Variant Calling * SNVs and small indels * HaplotypeCaller * Strelka2 * Structural variants * Manta * TIDDIT === ## Somatic Variant Calling * SNVs and small indels * Mutect2 * Strelka2 * Freebayes * Structural variants * Manta * Sample heterogeneity, ploidy and CNVs * ASCAT * Control-FREEC === ## Annotation * VEP and SnpEff * <i class="fas fa-database"></i> ClinVar, COSMIC, dbSNP, GENCODE, gnomAD, polyphen, sift, etc. === ## Reports [](https://multiqc.info/) <!-- .element class="image-H25" --> --- ## Workflow [](https://github.com/nf-core/sarek/releases/tag/2.5) <!-- .element class="image-25" --> --- ## Prioritization * First step towards clinical use * Rank scores are computed for all variants * COSMIC, ClinVar, SweFreq and MSK-IMPACT (cancerhotspots.org) * Findings are ranked * Well known, high-impact variants * Variants in known cancer-related genes * Remaining variants --- ## What's next * More tools * Mutational signatures * More downstream processing of the final vcf files * Connection to [Scout](https://www.clinicalgenomics.se/scout/) * More genomes * Mouse * Dog * Cattle Note: * Scout is a tool developed by SciLifeLab Clinical Genomics to analyse VCF files --- [](https://nf-co.re/) <!-- .element class="image-25" --> * Collection of High Quality Nextflow Pipelines * Strict guidelines * Extensive documentation * CI testing * Shared configuration --- ## Sarek usage * Within BTB * Tumor/normal pairs * In production at NGI * All normal samples * Tumor/normal pairs * The whole SweGen dataset * 1 000 normal samples (GRCh38) * Genome Medicine Sweden Note: * GMS is an initiative to implement Precision Medicine at a national level --- ## Preprint in BioRxiv Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants <small> Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I Olason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Diaz de Ståhl, Valtteri Wirta, Monica Nistèr, Björn Nystedt, Max Käller </small> [<i class="ai ai-doi"></i> doi.org/10.1101/316976](https://doi.org/10.1101/316976) --- ## Get involved * Our code is hosted on Github * [<i class="fab fa-github"></i> github.com/nf-core](https://github.com/nf-core) * [<i class="fab fa-github"></i> github.com/nf-core/sarek](https://github.com/nf-core/sarek) * We have slack * [<i class="fab fa-slack"></i> nfcore.slack.com](https://nfcore.slack.com/) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/sarek](https://nfcore.slack.com/channels/sarek) --- [](https://www.barncancerfonden.se/en/) <!-- .element class="image-H75" --> | [](https://www.ki.se/) <!-- .element class="image-H75" --> | [](https://ki.se/forskning/barntumorbanken) <!-- .element class="image-H75" --> | [](https://scilifelab.se/) <!-- .element class="image-H75" --> | [](https://uppmax.uu.se/) <!-- .element class="image-75" --> :-:|:-:|:-:|:-:|:-: ## Acknowledgments <small> Barntumörbanken | NGI | NBIS | Clinical Genomics | nf-core :-:|:-:|:-:|:-:|:-: Szilveszter Juhos | Johannes Alneberg | Malin Larsson | Hassan Foroughi Asl | Paolo Di Tommaso Monica Nistèr | Phil Ewels | Marcel Martin | Valtteri Wirta | Sven Fillinger Johanna Sandgren | Carl Rubin | Markus Mayrhofer | | Alexander Peltzer Teresita Díaz De Ståhl | Max Käller | Björn Nystedt | | </small> [](https://ngisweden.scilifelab.se/) <!-- .element class="image-H75" --> | [](https://www.nbis.se/) <!-- .element class="image-H75" --> | [](https://nf-co.re/) <!-- .element class="image-H75" --> | [](https://www.nextflow.io/) <!-- .element class="image-75" --> :-:|:-:|:-:|:-: --- <section data-background-image="https://maxulysse.github.io/assets/img/background/Stockholm-by-night.jpg" data-background-opacity=0.5 > ## Any questions * [<i class="fa fa-globe-europe"></i> nf-co.re](https://nf-co.re/) * [<i class="fab fa-github"></i> github.com/nf-core/sarek](https://github.com/nf-core/sarek) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/sarek](https://nfcore.slack.com/channels/sarek)