The last part of the DNA Pipeline combines the data from all the tubes and generates the sample-level VCF, .loom file, and other reports.
This process involves the following steps:
- Joint genotyping on all samples,
- Split multi-allelic variants into multiple records,
- Decompose complex variants,
- Remove blacklisted variants, and
- Loom file generation.
For more information on the Loom file generation, see this article in the Algorithm Overview section.