This part of the DNA Pipeline processes each tube individually and generates a VCF file as the final output.
The steps involved are:
- Adapter trimming,
- Barcode detection,
- Reference genome alignment,
- Barcode correction,
- Fixing mate read information,
- Cell detection, and
- Variant calling.
At the end of this step, a VCF file is generated for each tube. This file is then passed to the next step for the .loom file generation.