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    • DRAGEN v4.3
      • Getting Started
      • DRAGEN Host Software
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        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • CNV Output
          • CNV with SV Support
          • Multisample CNV Calling
          • Somatic CNV Calling WGS
          • Somatic CNV Calling WES
          • Allele Specific CNV for Somatic WES CNV
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
        • VNTR Calling
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
          • Effective Coverage Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single-Cell Pipeline
        • scRNA
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
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        • DNA Somatic Tumor-Normal Solid Panel
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  • Installation Requirements on the Host
  • Docker Runtime Arguments
  • Optional Docker Runtime Arguments

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  1. Product Guides
  2. DRAGEN v4.4
  3. Command Line Options

Docker Requirements

DRAGEN can be invoked from within a docker instance as long as the following conditions are met.

  1. DRAGEN is installed in the container.

  2. Installation requirements are met on the host.

  3. Required docker runtime arguments are passed.

Installation Requirements on the Host

Platform
Requirement

Onprem

Dragen must be installed on the host, and the version must be greater than or equal to the version in the container

AWS

dragen_drv must be installed on the host, and its version must be greater than or equal to the version required by DRAGEN. In DRAGEN 4.4 that is 1.4.8.13

Azure

XRT and Xilinx packages must be installed on the host

Docker Runtime Arguments

Docker runtime arguments are platform-specific.

Argument
Onprem
AWS
Azure

-v /dev/hugepages:/dev/hugepages:rw

yes

no

no

-v /dev/shm:/dev/shm:rw

yes

yes

yes

-v /etc/localtime:/etc/localtime

yes

no

no

-v /var/lib/edico:/var/lib/edico:rw

yes

no

no

-v /var/log/dragen:/var/log/dragen:rw

yes

no

no

-v /var/run/dragen:/var/run/dragen:rw

yes

no

no

--device /dev/bus

yes

yes

no

--device /dev/dri

no

no

yes

--pid host

yes

yes

yes

--ulimit nofile=720000:720000

yes

yes

yes

--ulimit nproc=16384:16384

yes

yes

yes

--ulimit memlock=4194304:4194304

yes

no

no

--ulimit stack=8192:8192

yes

yes

yes

Optional Docker Runtime Arguments

Argument
Description

--cap-add SYS_PTRACE

Allows DRAGEN to generate pstack files on failure, which helps with bug diagnosis

-v /dev/log:/dev/log

Redirects DRAGEN's syslog messages to the host's syslog daemon

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Last updated 2 days ago

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