gVCF/VCF Tyler Specification
Given a FASTA or a VCF/gVCF, give it a name.
Used by clinical labs to give variants names.
Questions that should be addressed by this story include:
- How does someone run this Tyler? (Is it a pipeline that someone runs on Arvados or a piece of software that someone downloads?)
- How does the user specify the reference? (Arvados collection hash, string, implicit in the input file)
- How does the software behave with poorly sequenced regions?
- What are the inputs/outputs? (Types of all of them, special requirements)
All these should be documented, at least in this ticket. Preferably the documentation can be done in the github repo: curoverse/lightning/docs (Create a new folder vcf-tyler or similar name), then linked to by this ticket.