Illumina Connected Software is becoming Illumina BioInsight Platform. For this and other updates, you can
read more here
Ctrlk
Illumina KnowledgeIllumina SupportSign In
For the complete documentation index, see llms.txt. This page is also available as Markdown.

DRAGEN Germline Whole Genome

Select the DRAGEN_Germline_Whole_Genome_4-5-4 Pipeline.

WARNING: Deviation from these instructions (including adding additional options) may cause pipeline failure.

  1. Select the necessary input files for the run, including sample inputs (.fastq, .fastq.ora, .bam, or .cram files), and a custom DRAGEN Reference Genome.

    1. Note: 5-base is compatible with any methyl_cg references. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.

  2. To Enable Methylation Aware Algorithms, select "True" for Enable 5-Base Methylation-Aware Algorithms.

  3. (Optional) To perform Small Variant Calling, set Enable Variant Caller to "True" and Emit Ref Confidence to "GVCF".

  4. If no Small Variant Calling is needed, set Enable Variant Caller to "False" and click the "X" next to Emit Ref Confidence.

  5. For Report Methylation at Variant Positions, select "default".

  6. (Optional) To perform CNV calling, set Enable CNV Calling to "True". Optionally turn on allele-specific CNV Calling.

  7. (Optional) To Enable SV Calling, select "True".

    1. NOTE: While SV Calling is validated as a stand alone option for DRAGEN Germline, they also improve CNV calling accuracy, and thus are recommended when running CNV Calling. .

  8. In the Additional Options section:

    1. (Optional) Check "Enable Variant Annotations" to turn on Nirvana Variant Annotation.

    2. (Optional) If downsampling is required, under Additional DRAGEN Commandline Argument, add --enable-fractional-down-sampler=true --down-sampler-normal-subsample=$Fraction, where $Fraction is a value between 0 and 1 representing the proportion of reads to keep.

    3. (Optional) Under Additional DRAGEN Commandline Arguments, add --gc-metrics-enable=true to enable GC metrics.

  9. Start the analysis.

PreviousICA Analysis Setup
NextDRAGEN Somatic

Last updated

Was this helpful?