DRAGEN Support Resources for Population Genomics

An informational page to get the latest DRAGEN pipeline versions and command lines used in large population genomics programs.

DRAGEN v3.7.8 user guide

Are you a researcher looking to produce the same results as All of Us Research Program, UK Biobank, or PRECISE (Singapore)?

The Illumina DRAGEN Bio-IT Platform provides accurate, comprehensive, and efficient secondary analysis of next-generation sequencing data. Some of the largest population genomics (PopGen) programs worldwide use DRAGEN for their secondary analysis.

This webpage gives you an overview of three large PopGen programs that use DRAGEN and the DRAGEN pipeline versions and command-line options used in these programs.

Access DRAGEN Germline for PopGen

Access the DRAGEN Germline for PopGen v3.7.8 in your deployment of choice

Whole Genome analysis by DRAGEN for population genomics initiatives

Get started with DRAGEN Germline for PopGen

This page is meant as a resource to help you set up your pipelines and avoid batch effects across cohorts. We recommend that you confirm these command-line options and versions with the respective PopGen programs.

Select
  • All of Us Research Program
  • PRECISE (Singapore)
  • UK Biobank
All of Us Research Program

Final Command for DRAGEN v3.7.8 Production

dragen \
-r <hg38-ref-dir/ \
--fastq-list <path-to>/fastq_list.csv \
--fastq-list-sample-id <id> \
--output-directory <out-dir> \
--output-file-prefix <prefix> \
--enable-variant-caller true \
--vc-emit-ref-confidence GVCF \
--vc-enable-vcf-output true \
--enable-duplicate-marking true \
--enable-map-align true \
--enable-map-align-output true \
--output-format CRAM \
--vc-hard-filter ‘DRAGENHardQUAL:all:QUAL<5.0;LowDepth:all:DP<=1’ \
--vc-frd-max-effective-depth=40 \
--vc-enable-joint-detection true \
--qc-cross-cont-vcf <path-to>/SNP_NCBI_GRCh38.vcf \
--qc-coverage-region-1 <path-to>/wgs_coverage_regions.hg38_minus_N.interval_list.bed \
--qc-coverage-reports-1 cov_report \
--qc-coverage-region-2 <path-to>/acmg59_allofus_19dec2019.GRC38.wGenes.NEW.bed \
--qc-coverage-reports-2 cov_report \
--qc-coverage-ignore-overlaps true
--qc-coverage-count-soft-clipped-bases true
--read-trimmers polyg
--soft-read-trimmers none

Output

Compare your VCF files to HG002 sample output data here

For Research Use Only. Not for use in diagnostic procedures.

PRECISE (Singapore)

Input

Download the input files

DRAGEN version 3.7.6 command line

/opt/edico/bin/dragen \
--lic-instance-id-location /opt/instance-identity \
--force \
--ref-dir /ephemeral/ref \
--fastq-list /mount/fastqlist/fastq_list.csv \
--output-file-prefix NPM1000045_55069 \
--output-directory /output \
--intermediate-results-dir /ephemeral/intermediate \
--output-format CRAM \
--enable-sort true \
--enable-duplicate-marking true \
--enable-map-align true \
--enable-map-align-output true \
--enable-variant-caller true \
--enable-vcf-compression true \
--vc-emit-ref-confidence GVCF \
--vc-enable-vcf-output true \
--vc-enable-joint-detection true \
--enable-metrics-json true \
--gc-metrics-enable true \
--qc-coverage-region-1 /mount/autosome/ReferenceAutosome.bed \
--qc-coverage-reports-1 overall_mean_cov hist contig_mean_cov cov_report callability \
--qc-coverage-filters-1 mapq<11,bq<0 \
--enable-sv true \
--enable-cnv true \
--cnv-enable-self-normalization true \
--cnv-segmentation-mode slm \
--auto-detect-sample-sex true \
--vc-enable-roh true \
--enable-cyp2d6 true \
--repeat-genotype-enable true \
--repeat-genotype-specs /opt/edico/repeat-specs/experimental/smn-catalog.hg38.json \
--qc-cross-cont-vcf /opt/edico/config/sample_cross_contamination_resource_hg38.vcf.gz

Output

Compare your VCF files to HG002 sample output data here

For Research Use Only. Not for use in diagnostic procedures.

UK Biobank

UKBB Command Line for DRAGEN

dragen \
-r <hg38-ref-dir> \
--bam-input <input BAM file> \
--output-directory <out-dir> \
--output-file-prefix <prefix> \
--enable-variant-caller=true \
--vc-emit-ref-confidence=GVCF \
--vc-enable-vcf-output=true \
--enable-duplicate-marking=true \
--enable-map-align=true \
--enable-map-align-output=true \
--output-format=CRAM \
--vc-hard-filter 'DRAGENHardQUAL:all:QUAL<5.0;LowDepth:all:DP<=1' \
--vc-frd-max-effective-depth=40 \
--qc-cross-cont-vcf <path-to>/SNP_NCBI_GRCh38.vcf \
--qc-coverage-region-1 <path-to>/wgs_coverage_regions.hg38_minus_N.interval_list.bed \
--qc-coverage-reports-1 cov_report \
--qc-coverage-region-2 <path-to>/acmg59_allofus_19dec2019.GRC38.wGenes.NEW.bed \
--qc-coverage-reports-2 cov_report \
--qc-coverage-ignore-overlaps=true \
--qc-coverage-count-soft-clipped-bases=true \
--read-trimmers polyg \
--soft-read-trimmers none \
--intermediate-results-dir=/ephemeral/staging/tmp/ \
--repeat-genotype-enable=true \
--enable-cyp2d6=true \
--enable-sv=true \
--enable-cnv=true \
--cnv-enable-self-normalization=true \
--vc-enable-joint-detection=true \

Output

Compare your VCF files to HG002 sample output data here

For Research Use Only. Not for use in diagnostic procedures.

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