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        • 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
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          • Mosaic Detection
          • VCF Imputation
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  • Germline WGS CNV Calling (ASCN) Options
  • Example command lines
  • Differences with respect to Germline WGS CNV (Depth-only)
  • Limitations

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  1. Product Guides
  2. DRAGEN v4.4
  3. DRAGEN DNA Pipeline
  4. Copy Number Variant Calling
  5. Available pipelines

Germline CNV Calling ASCN (WGS)

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Last updated 2 days ago

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The Germline WGS CNV caller (with Allele-Specific CN support) leverages depth of coverage and B-allele frequencies (BAFs) to detect germline copy number aberrations and regions with absence of heterozygosity (AOH).

The caller requires in input the sample to analyze and a catalog of population SNPs (used to estimate the B-allele frequencies across the genome). The output file is a VCF file. Several components of other germline CNV callers are reused, such as and counts estimation, correction, and . More details on the sample model selection are available in the section. See for more details on output files.

When enabled (default true), the caller can output an additional VCF with calls at resolutions compatible with cytogenetics technologies (e.g., ≥ 1 Mb, or whole-arm/whole-chromosome calls) For more information, see .

Germline WGS CNV Calling (ASCN) Options

You can use the following command-line options:

Option
Description

--fastq-file1,--fastq-file2,--bam-input, --cram-input

Specify an input file.

--cnv-population-b-allele-vcf

--enable-cnv

Enable or disable CNV processing. Set to true to enable CNV processing.

--enable-map-align

Enables the mapper and aligner module.

--output-directory

Output directory where all results are stored.

--output-file-prefix

Output file prefix that will be prepended to all result file names.

--ref-dir

The DRAGEN reference genome hashtable directory.

--sample-sex

If known, specify the sex of the sample. If the sample sex is not specified, the caller attempts to estimate the sample sex from alignments.

--cnv-enable-mosaic-calling

--cnv-enable-cyto-output

--cnv-enable-legacy-vcf-format

Use VCF v4.2 for CNV VCF output (default false).

--cnv-enable-self-normalization

Use self-normalization to normalize input sample.

Example command lines

The following is an example command line:

dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-map-align false \
--enable-cnv true \
--bam-input <BAM> \
--cnv-enable-self-normalization true \
--cnv-population-b-allele-vcf <SNV_POP_VCF> \
--sample-sex <SEX>

Differences with respect to Germline WGS CNV (Depth-only)

  • Whereas both the depth-only caller and the ASCN caller make use of a depth of coverage profile, the ASCN caller (but not the depth-only caller) additionally makes use of allelic read counts at sites along the genome provided through a population SNP catalog.

  • The ASCN caller segments both profiles (depth and BAF), then integrates their results. The depth-only caller only segments the depth profile.

  • The ASCN caller estimates the most likely diploid coverage for the input sample using both profiles (depth and BAF), while the depth-only caller has only the depth profile at its disposal.

  • The ASCN caller can also detect AOH/LOH regions and mosaic alterations, while the depth-only caller is limited to DEL and DUP regions.

Briefly, the following table summarizes the above differences:

Feature
Depth-only caller
ASCN caller

Coverage Depth Profile

âś“

âś“

B-Allele Frequency Profile

âś“

Coverage Depth Segmentation

âś“

âś“

B-Allele Frequency Segmentation

âś“

DEL/DUP Detection

âś“

âś“

Whole-arm/-chromosome Aneuploidy Detection

âś“ (Requires Cytogenetics Modality)

Whole-Genome Trisomy Detection

âś“

Minor-Allele Copy-Number Estimation

âś“

AOH/LOH Detection

âś“

Mosaic Alterations Detection

âś“

Limitations

The following features available in the non-ASCN germline caller are not yet supported:

  • Pedigree mode

  • Exome support

  • Star-Allele caller integration

  • Segmental Duplications extension

Specify a population SNP catalog. For more information on specifying b-allele loci, see .

Enable MOSAIC-calling mode (default true). For more information, see .

Enable Cytogenetics-compatible output (default true). For more information, see .

The Germline WGS ASCN caller differs from the in various respects:

depth-only caller
Cytogenetics Modality
segmentation
ASCN calling
Cytogenetics modality
Output Files
target
b-allele
bias
normalization
Specification of B-Allele Loci
MOSAIC-Calling Mode