MGvizCE: Clinical Exome QC and Analytics Pablo Marin-Garcia, Daniel Perez-Gil, Cristian Perez-Garcia, Alba Sanchis-Juan,Azahara Fuentes, Jose M. Juanes, Alberto Labarga, Antonio Fabregat, Vicente Arnau, Javier Chaves- Martinez, Javier Garcia-Planells and Ana Barbara Garcia-Garcia NGS facilities dedicated for clinical genomics need high QC standards, and they need continuously keeping track of their experiments and their metrics. As part of the Medical Genomics Visualization toolset (MGviz) we have developed an interactive software suit with R-Shiny and Python (Bokeh, crossfilter, flask and ReportLab) for automatic reports of QC for the whole NGS experiments in clinical diagnostics labs. The tool allows comparison of the current experiment with historic data to see the performance of the sequencher, checking different metrics for coverage and variations, warning for large copy number regions In addition it remembers decisions over annotations, helps in variant prioritization, segregation and finding compound heterozygotes and make automatic historical reports of pathogenic variants informed by the lab. NGS QC: ENAC accreditation in Process - Automatic report after pipeline finishes. - Interactive coverage exploration. - All information of the NGS QC metrics stored in Mongodb and sqlite - Automatic report after pipeline finishes. - Interactive coverage exploration. - All information of the NGS QC metrics stored in Mongodb and sqlite Finding CNVs in Cancer Control Discordant profile QC from historical Data Check Sex Find CNVs Report coverage and gaps DNA agarose Degraded Amplicons Exome Gaps from historic p75 Gaps cov <20 Area historic percentil25-75 Cov sample Area historic percentil25-75 Historical coverage per run Comparing against historic profiles we can detect degraded DNA or other artifacts Summary MGviz is a web and CLI tool very useful for QC and analytics for exome and amplicon NGS. Here we have shown only the QC and visualization tools. Code will be released in July at github. Doi: /m9.figshare

Workflow FASTQ Sex checkout Data + Barcodes PCR Capture Nextera Blood stock Stock DNA Working dilution DNA extraction Dilution Amplicon Analysis Exome Analysis DNA degradation