Project

General

Profile

Actions

Story #15996

closed

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

Added by Peter Amstutz about 3 years ago. Updated over 2 years ago.

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

100%

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 1 (0 open1 closed)

Task #15997: ReviewResolvedNico C├ęsar01/29/2020

Actions

Related issues

Related to Arvados Epics - Story #15961: End-to-end demoResolved01/15/202001/31/2021

Actions
Actions #1

Updated by Peter Amstutz about 3 years ago

  • Status changed from New to In Progress
Actions #2

Updated by Peter Amstutz about 3 years ago

  • Assigned To set to Bryan Cosca
  • Status changed from In Progress to New
  • Category set to Sample Pipelines
Actions #3

Updated by Peter Amstutz about 3 years ago

  • Description updated (diff)
Actions #4

Updated by Bryan Cosca about 3 years ago

  • Status changed from New to In Progress
Actions #6

Updated by Peter Amstutz about 3 years ago

  • Description updated (diff)
Actions #7

Updated by Peter Amstutz about 3 years ago

Actions #8

Updated by Peter Amstutz about 3 years ago

  • Target version changed from 2020-01-15 Sprint to 2020-01-29 Sprint
Actions #9

Updated by Peter Amstutz about 3 years ago

  • Description updated (diff)
Actions #10

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-01-29 Sprint to 2020-02-12 Sprint
Actions #11

Updated by Peter Amstutz almost 3 years ago

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

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-02-26 Sprint to 2020-03-11 Sprint
Actions #13

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-03-11 Sprint to 2020-03-25 Sprint
Actions #14

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-03-25 Sprint to 2020-04-08 Sprint
Actions #15

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-04-08 Sprint to 2020-04-22
Actions #16

Updated by Peter Amstutz almost 3 years ago

  • Assigned To changed from Bryan Cosca to Sarah Zaranek
Actions #17

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2020-04-22 to 2020-05-06 Sprint
Actions #18

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-05-06 Sprint to 2020-05-20 Sprint
Actions #19

Updated by Peter Amstutz over 2 years ago

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

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint
Actions #21

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint
Actions #22

Updated by Sarah Zaranek over 2 years ago

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

Actions #23

Updated by Sarah Zaranek over 2 years 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)

Actions #24

Updated by Sarah Zaranek over 2 years 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)
Actions #25

Updated by Sarah Zaranek over 2 years 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)
Actions #26

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-07-01 Sprint to 2020-07-15
Actions #27

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-07-15 to 2020-08-12 Sprint
Actions #28

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-08-12 Sprint to 2020-08-26 Sprint
Actions #29

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2020-08-26 Sprint to 2020-09-09 Sprint
Actions #30

Updated by Peter Amstutz over 2 years ago

  • Status changed from In Progress to Resolved
Actions

Also available in: Atom PDF