Workflow: Whole Genome Sequence processing workflow scattered over samples

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<p>This is a “real-world” workflow example for processing Next Generation Sequencing (NGS) Whole Genome Sequence (WGS) data.</p> <p>You can learn more and run this workflow yourself by going through the <a href=\"https://doc.arvados.org/main/user/tutorials/wgs-tutorial.html\">Processing Whole Genome Sequences</a> walkthrough in the Arvados user guide.</p> <p>The steps of this workflow include:</p> <ol> <li>Check of fastq quality using FastQC</li> <li>Local alignment using BWA-MEM</li> <li>Variant calling in parallel using GATK Haplotype Caller</li> <li>Generation of an HTML report comparing variants against ClinVar archive</li> </ol> <p>The primary input parameter is the <b>Directory of paired FASTQ files</b>, which should contain paired FASTQ files (suffixed with _1 and _2) to be processed. The workflow scatters over the samples to process them in parallel.</p> <p>The remaining parameters are reference data used by various tools in the pipeline.</p>

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