[annotation] Stitch Together VCF Files - Second Step

[akotlar]

Background:

A concise description of why we're pursuing this task.

Users has different waves of data, like different batches. So they want to be able to handle vcf stitching in phases. They may have chromosome chr1 processed, and want to annotate it. Now they get chromosome chr2 and want to add to the existing annotation / index.

They will want to get annotation, index, genotype dosage matrix primarily. They may want to get a stitched VCF output as well. As part of this, we should be able to roundtrip a VCF file (VCF -> annotation -> VCF) as well (but do this in a separate ticket).

They may come from different paths.

Completion Criteria:

What is the goal, and how do we know this task is accomplished?

Implementation Summary

Give enough technical detail for a teammate to understand the proposed solution.