Idea #15996
closed
human WGS fastq to gvcf variant calling with GATK4 CWL (with report)
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.
Related issues
Updated by Peter Amstutz over 4 years ago
- Status changed from New to In Progress
Updated by Peter Amstutz over 4 years ago
- Assigned To set to Bryan Cosca
- Status changed from In Progress to New
- Category set to Sample Pipelines
Updated by Bryan Cosca
Updated by Sarah Zaranek over 4 years ago
Links to collections with BAMS:
PGP Veritas
https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-1rqqi0kpkfmfite
Simons Diversity
https://workbench.su92l.arvadosapi.com/projects/su92l-j7d0g-8jz57m90mutkdwv
Updated by Peter Amstutz over 4 years ago
- Related to Idea #15961: End-to-end demo added
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-01-15 Sprint to 2020-01-29 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-01-29 Sprint to 2020-02-12 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-02-12 Sprint to 2020-02-26 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-02-26 Sprint to 2020-03-11 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-03-11 Sprint to 2020-03-25 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-03-25 Sprint to 2020-04-08 Sprint
Updated by Peter Amstutz about 4 years ago
- Target version changed from 2020-04-08 Sprint to 2020-04-22
Updated by Peter Amstutz about 4 years ago
- Assigned To changed from Bryan Cosca to Sarah Zaranek
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-04-22 to 2020-05-06 Sprint
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-05-06 Sprint to 2020-05-20 Sprint
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-05-20 Sprint to 2020-06-03 Sprint
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint
Updated by Sarah Zaranek almost 4 years ago
Demo is finished nearly and is located in arvados-tutorial repo under WGS-processing
Updated by Sarah Zaranek almost 4 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)
Updated by Sarah Zaranek almost 4 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)
Updated by Sarah Zaranek almost 4 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)
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-07-01 Sprint to 2020-07-15
Updated by Peter Amstutz almost 4 years ago
- Target version changed from 2020-07-15 to 2020-08-12 Sprint
Updated by Peter Amstutz over 3 years ago
- Target version changed from 2020-08-12 Sprint to 2020-08-26 Sprint
Updated by Peter Amstutz over 3 years ago
- Target version changed from 2020-08-26 Sprint to 2020-09-09 Sprint
Updated by Peter Amstutz over 3 years ago
- Status changed from In Progress to Resolved