Identify and Annotate Variants (WES)

The Identify and Annotate Variants (WES) template workflow should be used to identify and annotate variants in one sample. The workflow is a combination of the Identify Variants and the Annotate Variants workflows.

The workflow starts with mapping the sequencing reads to the human reference sequence, followed by a local realignment to improve the variant detection that is run afterwards. After the variants have been detected, they are annotated with gene names, amino acid changes, conservation scores, information from relevant variants present in the ClinVar database, and information from common variants present in the common dbSNP Common, HapMap, and 1000 Genomes database. Furthermore, a detailed targeted region coverage report is created to inspect the overall coverage and mapping specificity.

Before starting the workflow, you will need to import in the CLC Workbench a file with the genomic regions targeted by the amplicon or hybridization kit. Such a file (a BED or GFF file) is usually available from the vendor of the enrichment kit and sequencing machine. Use the Import | Tracks tool to import it in your Navigation Area.


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