Post on 29-Jul-2018
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 theirmetrics. 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 allowscomparison of the current experiment with historic data to see the performance of the sequencer, checking different metrics for coverage andvariations, 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
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 percentil25-75Cov sample Area historic percentil25-75
Historical coverage per run
Comparing against historic profiles we can detect degraded DNA or other artifacts
SummaryMGviz is a web and CLI tool very useful for QC andanalytics for exome and amplicon NGS. Here we haveshown only the QC and visualization tools.
Code will be released on July at github. https://github.com/MGviz-‐soft
pablo.marin@uv.es Doi: 10.6084/m9.figshare.3369787
Tumor Blood