Story #15996

human WGS fastq to gvcf variant calling with GATK4 CWL (with report)

Added by Peter Amstutz 7 months ago. Updated 26 days 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 Progress01/15/202008/26/2020

History

#1 Updated by Peter Amstutz 7 months ago

  • Status changed from New to In Progress

#2 Updated by Peter Amstutz 7 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 7 months ago

  • Description updated (diff)

#4 Updated by Bryan Cosca 7 months ago

  • Status changed from New to In Progress

#6 Updated by Peter Amstutz 7 months ago

  • Description updated (diff)

#7 Updated by Peter Amstutz 7 months ago

#8 Updated by Peter Amstutz 7 months ago

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

#9 Updated by Peter Amstutz 7 months ago

  • Description updated (diff)

#10 Updated by Peter Amstutz 6 months ago

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

#11 Updated by Peter Amstutz 6 months ago

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

#12 Updated by Peter Amstutz 6 months ago

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

#13 Updated by Peter Amstutz 5 months ago

  • Target version changed from 2020-03-11 Sprint to 2020-03-25 Sprint

#14 Updated by Peter Amstutz 5 months ago

  • Target version changed from 2020-03-25 Sprint to 2020-04-08 Sprint

#15 Updated by Peter Amstutz 4 months ago

  • Target version changed from 2020-04-08 Sprint to 2020-04-22

#16 Updated by Peter Amstutz 4 months ago

  • Assigned To changed from Bryan Cosca to Sarah Zaranek

#17 Updated by Peter Amstutz 4 months ago

  • Target version changed from 2020-04-22 to 2020-05-06 Sprint

#18 Updated by Peter Amstutz 3 months ago

  • Target version changed from 2020-05-06 Sprint to 2020-05-20 Sprint

#19 Updated by Peter Amstutz 3 months ago

  • Target version changed from 2020-05-20 Sprint to 2020-06-03 Sprint

#20 Updated by Peter Amstutz 2 months ago

  • Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint

#21 Updated by Peter Amstutz about 2 months ago

  • Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint

#22 Updated by Sarah Zaranek about 2 months ago

Demo is finished nearly and is located in arvados-tutorial repo under WGS-processing

#23 Updated by Sarah Zaranek about 2 months ago

Files to review:

wgs-processing-wf.cwl
getfastq.cwl
bwamem-gatk-report-wf.cwl
fastqc.cwl
bwamem-samtools-view.cwl
samtools-sort.cwl
mark-duplicates.cwl
samtools-index.cwl

And readme.md and associated code in src

Currently Labeling/Adding Metadata to:
scatter-gatk-wf-with-interval.cwl (and subworkflows)
report-wf.cwl (and subworkflows)

#24 Updated by Sarah Zaranek about 2 months ago

  • Subject changed from human exome/WGS fastq to gvcf variant calling with GATK4 CWL to human exome/WGS fastq to gvcf variant calling with GATK4 CWL (with report)

#25 Updated by Sarah Zaranek about 2 months ago

  • Subject changed from human exome/WGS fastq to gvcf variant calling with GATK4 CWL (with report) to human WGS fastq to gvcf variant calling with GATK4 CWL (with report)

#26 Updated by Peter Amstutz about 1 month ago

  • Target version changed from 2020-07-01 Sprint to 2020-07-15

#27 Updated by Peter Amstutz 26 days ago

  • Target version changed from 2020-07-15 to 2020-08-12 Sprint

Also available in: Atom PDF