Story #7488

gVCF/VCF Tyler Specification

Added by Sarah Guthrie over 3 years ago. Updated about 1 year ago.

Status:
Closed
Priority:
Normal
Assigned To:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
1.0

Description

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.

History

#1 Updated by Sarah Guthrie over 3 years ago

  • Subject changed from gVCF Tyler Specification and Implementation to gVCF/VCF Tyler Specification and Implementation

#2 Updated by Sarah Guthrie over 3 years ago

  • Project changed from Curoverse Science to Lightning

#3 Updated by Sarah Guthrie over 3 years ago

  • Subject changed from gVCF/VCF Tyler Specification and Implementation to gVCF/VCF Tyler Specification
  • Story points changed from 2.0 to 1.0

#4 Updated by Sarah Guthrie over 3 years ago

  • Description updated (diff)

#5 Updated by Sarah Guthrie over 3 years ago

  • Description updated (diff)

#6 Updated by Sarah Guthrie over 3 years ago

  • Target version changed from 2015-11-13 Lightning sprint to Future sprints (Lightning)

#7 Updated by Sarah Zaranek about 1 year ago

  • Status changed from New to Closed

Closing this out for now.

Also available in: Atom PDF