> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs-umi.md). # 5 Base DNA Germline WGS UMI A DRAGEN recipe, like this one, is a predefined set of analysis parameters and workflow settings tailored to a specific type of genomic analysis. For clarity, some default parameters are explicitly included and annotated with comments. ``` /opt/dragen/$VERSION/bin/dragen #DRAGEN install path --ref-dir $REF_DIR #path to DRAGEN pangenome hashtable --output-directory $OUTPUT --intermediate-results-dir $PATH #e.g. SSD /staging --output-file-prefix $PREFIX # Inputs --fastq-list $PATH #see 'Input Options' for FQ, BAM or CRAM --fastq-list-sample-id $STRING # Mapper --enable-map-align true #optional with BAM/CRAM input --enable-map-align-output true #optionally save the output BAM --enable-sort true #default=true # UMI --umi-enable true --umi-min-supporting-reads 1 #Default=2 # 5-Base --methylation-conversion illumina --methylation-generate-cytosine-report true --methylation-compress-cx-report true # Small variant caller --enable-variant-caller true # Annotation --variant-annotation-data PATH --enable-variant-annotation true # SV --enable-sv true # CNV --enable-cnv true --cnv-enable-self-normalization true ``` ## Notes and additional options ### Hashtable For DRAGEN germline runs, it is recommended to use the pangenome hashtable. See: [Product Files](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html) ### Input options DRAGEN input sources include: fastq list, fastq, bam, or cram. For BCL input, first create FASTQs using [BCL conversion](/dragen-v4.4/product-guide/dragen-v4.4/bcl-conversion.md). FQ list Input ``` --fastq-list $PATH --fastq-list-sample-id $STRING ``` FQ Input ``` --fastq-file1 $PATH --fastq-file2 $PATH --RGSM $STRING --RGID $STRING ``` BAM Input ``` --bam-input $PATH ``` CRAM Input ``` --cram-input $PATH ``` ### Mapping and Aligning | Option | Description | | -------------------------------- | ---------------------------------------------------------------------------------------------------- | | `--enable-map-align true` | Optionally disable map & align (default=true). | | `--enable-map-align-output true` | Optionally save the output BAM (default=false). | | `--Aligner.clip-pe-overhang 2` | Clean up any unwanted UMI indexes. Only use when reads contain UMIs, but UMI collapsing was not run. | ### UMI | Option | Description | | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `--umi-nonrandom-whitelist $PATH` | If UMI is nonrandom, either a whitelist or correction table is required. The whitelist includes a valid UMI sequence per line. | | `--umi-correction-table $PATH` | If UMI is nonrandom, either a whitelist or correction table is required. The correction table defaults to the table used by TruSight Oncology: \/resources/umi/umi\_correction\_table.txt.gz. | | `--umi-min-supporting-reads INT` | Specify the number of matching UMI input reads required to generate a consensus read. Any family with insufficient supporting reads is discarded. The default is 2, but most pipelines perform better with this setting set to 1. A setting of 2 may potentially be relevant for samples with ultra deep coverage (e.g. ctDNA). | | `--umi-metrics-interval-file $BED` | Target region in BED format. | | `--umi-emit-multiplicity both` | Set the consensus sequence type to output. DRAGEN UMI allows collapsing duplex sequences from the two strands of the original molecules. For more information, see [Merge Duplex UMIs](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers.md#merge-duplex-umis). | | `--umi-start-mask-length INT` | Number of additional bases to ignore from start of read. The default is 0. To reduce FP optionally set to 1. | | `--umi-end-mask-length INT` | Number of additional bases to ignore from end of read. The default is 0. To reduce FP optionally set to 3. | For more information see: [UMI Options](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers.md#umi-options). ### 5-Base Methylation | Option | Description | | --------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `--methylation-conversion STRING` | Library conversion for methylation analysis. Options: `none`, `c_t`, `mc_t`, `illumina` (default=none). | | `--methylation-protocol STRING` | Library protocol for methylation analysis. Options: `none`, `directional`, `non-directional`, `directional-complement`, `pbat`. The default value for `methylation-conversion=illumina` is `directional`, otherwise it is `none`. | | `--methylation-mapq-threshold INT` | Only reads with MAPQ greater or equal than the threshold will be included in methyl-seq analysis (default=0). | | `--methylation-generate-mbias-report true` | Whether to generate a per-sequencer-cycle methylation bias report (default=true). | | `--mbias-report-include-overlaps` | Calculate methylation stats for overlapping bases between mates (default=false). | | `--methylation-generate-cytosine-report true` | Whether to generate a genome-wide cytosine methylation CX\_report file (default=false). | | `--methylation-compress-cx-report true` | Set to true to enable compression of the CX\_report (default=true). | | `--methylation-keep-ref-cytosine true` | Set to true to keep all reference cytosines in the CX\_report file, even if they don't appear in the input reads (default=false). | | `--enable-cpg-methylated-mapping true` | Enable methylated mapping with base conversions restricted to CpG context (default=true). When false, runs DRAGEN Methylation 3-base map/align instead. | | `--methylation-report-to-vcf` | Specify methylation type (none, cg, or c) which is reported in VCF files (default=c). | | `--methylation-report-to-gvcf` | Specify methylation type (none, cg, or c) which is reported in gVCF files (default=cg). | For more information see: [5-Base Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline.md). ### SNV | Option | Description | | ------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------- | | `--vc-target-bed` | Limit variant calling to region of interest. | | `--vc-combine-phased-variants-distance INT` | Maximum distance in base pairs (BP) over which phased variants will be combined. Set to 0 to disable. Valid range is \[0; 15] BP (Default=2) | For more detail on the small variant caller in somatic mode please refer to [Somatic Mode](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) ### Annotation For instructions on how to download the Nirvana annotation database, please refer to [Nirvana](/dragen-v4.4/product-guide/dragen-v4.4/nirvana.md) ### CNV | Option | Description | | ------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- | | `--cnv-enable-gcbias-correction true` | Enable or disable GC bias correction when generating target counts. | | `--cnv-segmentation-mode $SEG_MODE` | Option to override the default segmentation algorithm. Defaults include `slm` for germline WGS, `aslm` for somatic WGS, and `hslm` for targeted analysis. | For more information, see [CNV Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling.md). --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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