Identify Known Variants in One Sample (TAS)
The Identify Known Variants in One Sample (TAS) template workflow combines data analysis and interpretation. It should be used to identify known variants as specified by the user (e.g., known breast cancer associated variants) for their presence or absence in a sample. This workflow will not identify new variants.
The workflow maps the sequencing reads to a human genome sequence and does a local realignment of the mapped reads to improve the subsequent variant detection. In the next step, only variants specified by the user are identified and annotated in the newly generated read mapping.
Before starting the workflow, you may need to import your the following files with the Import | Tracks tool (see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Import_tracks.html):
- Import your known variants. Variants can be imported in GVF or VCF format.
- Import your targeted regions. A file with the genomic regions targeted by the amplicon or hybridization kit can usually be provided by the vendor, either BED or GFF format.
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