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.

The .loom file generated in this step can be visualized using Tapestri Insights or used for copy number or loss of heterozygosity (LOH) analysis using Mosaic.

For more information on the Loom file generation, see this article in the Algorithm Overview section.