The tool runs an internal workflow, which starts with mapping the sequencing reads to the human reference sequence. Then it runs a local realignment to improve the variant detection, which 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, HapMap, and 1000 Genomes database. Furthermore, a targeted region report is created to inspect the overall coverage and mapping specificity.
The difference between Identify and Annotate Variants (TAS-HD) and (WES-HD) is that the Autodetect paired distances has been switched off in Map Reads to Reference tool for the TAS workflows.
- How to run the Identify and Annotate Variants (TAS-HD) workflow
- Output from the Identify and Annotate Variants (TAS-HD) workflow