Portable pipeline for whole exome and genome sequencing
Creators: name: Isaev, Timur
name: Kokorev, Andrey
name: Krier, Joel
name: Magee, Patrick
name: Ward, Heather
name: Arezou A. Ghazani
name: Bouzinier, Michael
Publisher: name: F1000 Research Limited
Year: 2019

description: Summary<br>Genomic sequencing is an important part of modern healthcare, and bioinformatics pipelines are now an essential part of the diagnostic process. Portable pipelines can be easily shared between different teams and address important issues such as the reproducibility of the results. <br>A pipeline for processing Whole Genome and Whole Exome cases was developed at Sunyaev Lab at Harvard Medical School and Brigham &amp; Women's Hospital and is being used by several clinical institutions. Following the GATK best practices and using GATK 3.x for calling common variants, the pipeline also uses a set of rare variant callers to look for uncommon variants. Finally, the pipeline annotates variants to be loaded into Variant Curation Tools. <br>We present a WDL version of the original pipeline achieving greater portability and providing reproducibility of the results in various environments. Using GATK4, it takes FASTQ raw sequencing data and produces a VCF file, ready to be ingested by tools such as xBrowse or Forome Anfisa annotation and variant curation suite.<br>We have tested the workflow in various computational environments supported by Cromwell. By porting the end-to-end pipeline to WDL, we hope to help promote Cromwell to the broader bioinformatics community.<br><br>Full Abstract<br>Genomic sequencing is an important part of modern healthcare, making bioinformatics pipelines an essential part of the diagnostic process. <br>With the advancement in technologies, it became possible to perform sequencing at a fast rate. Processing raw sequence data to find genomic variants plays a significant role in diagnostics, identifying optimal treatments, and understanding the nature of diseases. This makes bioinformatics pipelines an essential part of the genomic analysis. However, to be adopted for clinical practice, pipelines should comply with strict reproducibility requirements. Creating fully portable pipelines, that can be easily shared and used by different teams in various computational environments, allowing researchers and clinicians to reproduce each other's results, helps in moving towards standardizing this process. An additional benefit of portability is saving researchers time and costly investments for the development of their own pipelines. In recent years there has been a noticeable push to develop portable pipelines [1,2]. In particular GA4GH (Global Alliance for Genomics and Health) and it’s Cloud Containers and Workflows workstream has played a significant role in advancing the principles of portability, interoperability and reproducibility of results [3]. Our fully open source pipeline is focused on processing human Whole Genome and Whole Exome cases and producing both clinical results and research data that is used for medical diagnostics through gene discovery.<br>Originally, the pipeline was developed at Sunyaev Lab at the Department of Biomedical Informatics at Harvard Medical School and Genetics Division of Brigham &amp; Women's Hospital and is being used by several clinical institutions [5]. As input, it takes raw sequencing data in FASTQ or BAM format. The pipeline consists of three distinct components: Upstream, creating the aligned BAM files and calling common variants using GATK 3.x. A set of custom variant callers identifies extremely rare and unknown variants in a pedigree-aware way. This component includes a De-Novo caller[7] for identifying de novo mutations (mutations that are present for the first time in one family member). The downstream component annotates the variants with a wide range of information related to functional analysis, population genetics, clinical knowledge, epigenetics, etc. The resulting VCF is ready to be ingested by variant curation tools like xBrowse or Forome Anfisa. An optional last step in the pipeline can directly load the case into Anfisa. <br>While the pipeline was originally developed for Sun Grid Engine environment, the portable version of the pipeline that we present is written in WDL (Workflow Description Language) and exclusively uses GATK4. It can be executed with Cromwell [4] in any environment supported by Cromwell. We have successfully run cases on our local cluster and on Google Cloud using the DNAStack platform. Testing in the AWS version of Cromwell uncovered several issues in the AWS implementation that are currently being addressed by AWS and Broad Institute teams, prospectively making it a more stable release for the growing Cromwell community.<br>To summarize, the pipeline provides a portable workflow for converting the raw sequencing data in FASTQ format to results usable in a clinical environment. In combination with the Forome Anfisa Variant Curation Tool, it can yield a clinically actionable report. It is used on a routine basis by BGM [5] and SEQaBOO [6] projects.<br>Our team was among the first to adopt WDL and Cromwell for portable bioinformatics pipelines from upstream to downstream and publish them for the benefit of the open source community. The pipeline is being actively promoted within the Undiagnosed Disease Network bioinformatics community. <br>The WDL workflow for the pipeline comes under the Apache 2.0 license and is available on GitHub in the Forome Association repository: https://github.com/ForomePlatform/pipeline <br><br>References: Fjukstad B, Bongo LA. 2017. A review of scalable bioinformatics pipelines. Data Science and Engineering 2 (3), 245-251 Causey JL, Ashby C, Walker K, et al. DNAp: A Pipeline for DNA-seq Data Analysis. Sci Rep. 2018;8(1):6793. doi:10.1038/s41598-018-25022-6. Brian D O’Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Liu X. K, Patricia J, Paten B, Stein L, Ferretti V. The dockstore: enabling modular, community focused sharing of docker-based genomics tools and workflows. F1000Research, 6, 2017 Voss K, Gentry J, Van dAG. Full-stack genomics pipelining with GATK4 + WDL + Cromwell 2017. Available from: https://f1000research.com/posters/6-1379. Haghighi A., Krier J.B., Toth-Petroczy A., Cassa C.A., Frank N.Y., Carmichael N., Fieg E., Bjonnes A., Mohanty A., Briere L.C.et al. An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genome Med. 2018 SEQaBOO - SEQuencing a Baby for an Optimal Outcome (http://seqaboo.bwh.harvard.edu/), under the NIH grant R01-DC015052-01 Mohanty A, Vuzman D, Francioli L, Cassa C, Toth-Petroczy A, Sunyaev S. August 2018, novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data