Story #15996

human exome/WGS fastq to gvcf variant calling with GATK4 CWL

Added by Peter Amstutz about 2 months ago. Updated 1 day ago.

Status:
In Progress
Priority:
Normal
Assigned To:
Category:
Sample Pipelines
Target version:
Start date:
01/29/2020
Due date:
% Done:

0%

Estimated time:
(Total: 0.00 h)
Story points:
-

Description

Find community-built best practices GATK4 variant calling CWL and/or create one from scratch

Run on several PGP samples using su92l

Put everything in a public project and document it thoroughly.

Do some reporting (Multi-QC) and automated interpretation (CLINVAR annotation with SnpEff?)

Stretch goals:

Second pipeline using Deep Variant

gVCF output is suitable to feed directly into the Lightning CWL for tiling.


Subtasks

Task #15997: ReviewNewPeter Amstutz


Related issues

Related to Arvados Epics - Story #15961: End-to-end demoIn Progress01/15/202003/31/2020

History

#1 Updated by Peter Amstutz about 2 months ago

  • Status changed from New to In Progress

#2 Updated by Peter Amstutz about 2 months ago

  • Assigned To set to Bryan Cosca
  • Status changed from In Progress to New
  • Category set to Sample Pipelines

#3 Updated by Peter Amstutz about 2 months ago

  • Description updated (diff)

#4 Updated by Bryan Cosca about 2 months ago

  • Status changed from New to In Progress

#6 Updated by Peter Amstutz about 2 months ago

  • Description updated (diff)

#7 Updated by Peter Amstutz about 1 month ago

#8 Updated by Peter Amstutz about 1 month ago

  • Target version changed from 2020-01-15 Sprint to 2020-01-29 Sprint

#9 Updated by Peter Amstutz about 1 month ago

  • Description updated (diff)

#10 Updated by Peter Amstutz 30 days ago

  • Target version changed from 2020-01-29 Sprint to 2020-02-12 Sprint

#11 Updated by Peter Amstutz 16 days ago

  • Target version changed from 2020-02-12 Sprint to 2020-02-26 Sprint

#12 Updated by Peter Amstutz 1 day ago

  • Target version changed from 2020-02-26 Sprint to 2020-03-11 Sprint

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