The QIAGEN GeneRead Panel Analysis is a ready-to-use workflow that can identify and annotate variants in Targeted Amplicon Sequencing data generated with GeneRead DNAseq Gene Panels. The GeneRead DNAseq Gene Panels can either be standard panels focused on a specific set of genes or can be customized to include genes tailored to specific research interests.
The first step in the ready-to-use workflow is mapping of the sequencing reads to the human reference sequence. This is followed by a local realignment step, which is included to improve the variant detection that follows directly after a primer trimming step. After variant detection, the variants are annotated with gene names, exon numbers, amino acid changes, conservation scores, information from relevant variants present in the ClinVar database, and information from common variants present in the common dbSNP, HapMap, and 1000 Genomes database. Furthermore, a detailed target regions mapping report is created that allows inspection of the coverage and mapping specificity in the target regions.
The QIAGEN GeneRead Panel Analysis workflow assumes that the sequences used as input do not contain adapters as the removal of adapters is often done directly on the sequencing machine. If adapters have not been trimmed off, please do so before proceeding with your analysis by using the Trim Reads tool (from the "Prepare Raw Data" folder) with the "Automatic read-through adapter trimming" option enabled.