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 the tapestri R package.

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