DragenGE

Introduction

A pipeline to perform joint calling on targetted enrichment NGS data on the Dragen server.

Calls SNPs/Indels

Updated for Human Reference Genome Build GRCh38

Requirements

dragen Version (Software Release v3.7)

Run

The script should be run on a per sample basis in a directory structure such as this:

IlluminaTruSightOne/
├── sample1/
│   ├── sample1_S1_L001_R1_001.fastq.gz
│   ├── sample1_S1_L001_R2_001.fastq.gz
│   ├── sample1_S2_L002_R1_001.fastq.gz
│   ├── sample1_S2_L002_R2_001.fastq.gz
│   └── sample1.variables

This can be found within the staging area fastq directory on the Dragen e.g. /staging/data/fastq/191010_D00501_0366_BH5JWHBCX3/Data/IlluminaTruSightOne

Once within this folder:

bash DragenGE.sh $sample_folder_location

Where $sample_folder_location is something like /staging/data/fastq/191010_D00501_0366_BH5JWHBCX3/Data/IlluminaTruSightOne/sample1

Once the gvcf creation is complete for each sample the joint genotyping will be called and produce the final joint vcf.

Results

Produces results in:

/staging/data/results/$run_id/$panel/

Will produce:

Sample Level:

• BAM file
• QC Metrics

Run Level:

• Joint VCF
• Joint VCF hard filtered
• Variant Calling Metrics

Authors

Chris Medway and Joseph Halstead

References

https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/dragen-bio-it/dragen-bio-it-platform-user-guide-1000000070494-06.pdf