Our advanced variant analysis pipelines use the academic or industry standard as the starting point and extend them with advanced features and functionalities.
We follow a process similar to the standard BWA-Picard-GATK workflow, substituting with a few well-tested tools/stages with faster, resource-optimized (RAM, storage), cloud-friendly alternatives. In addition, we also deploy a combined variant calling strategy using multiple callers to maximize the diagnostic rate, reliability and to minimize false detections.
We specialize in CNV detection from whole-exome, whole-genome and targetted gene panel data. We have handled CNV analysis in several large-scale projects.
Our bespoke workflows offer CNV analysis together with sample QC, pre-, and post-CNV detection QC, filtering and disease biology for various common and rare diseases. We have also handled cancer samples (FFPE and Fresh Frozen tissues) for which we have developed customized QC and analysis.
We use a combination of tools depending on the end users’ requirements. We make use of this data not only for the analysis of disease biology, but also for the detection of contamination, sample/data quality, etc.
From the detection of Trisomies and UPDs, we use multiple analysis methods/tools for whole-genome, whole-exome, gene panels and arrays.