Germline CNV Calling ASCN (WGS)

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 target and b-allele counts estimation, bias correction, normalization and segmentation. More details on the sample model selection are available in the ASCN calling section. See Output Files 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 Cytogenetics modality.

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	Specify a population SNP catalog. For more information on specifying b-allele loci, see Specification of B-Allele Loci.
--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	Enable MOSAIC-calling mode (default true). For more information, see MOSAIC-Calling Mode.
--cnv-enable-cyto-output	Enable Cytogenetics-compatible output (default true). For more information, see Cytogenetics Modality.
--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)

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

• 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	✓	✓
B-Allele Frequency Profile		✓
Coverage Depth Segmentation	✓	✓
B-Allele Frequency Segmentation		✓
DEL/DUP Detection	✓	✓
Whole-arm/-chromosome Aneuploidy Detection		✓ (Requires Cytogenetics Modality)
Whole-Genome Trisomy Detection		✓
Minor-Allele Copy-Number Estimation		✓
AOH/LOH Detection		✓
Mosaic Alterations Detection		✓

Limitations

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

• Pedigree mode

• Exome support

• Star-Allele caller integration

Examples

The following are some examples of calls that can be output by the germline WGS ASCN caller:

# REF call
chr1    819841  DRAGEN:REF:chr1:819841-4063702  N       .       1000    PASS
  END=4063702;REFLEN=3243862
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  0/0:2:1:1000:1000:2.00155:1.000775:1.000775:129.1:0.5:2661:6145:66,5:0.0037637

# Copy-neutral LOH call
chr1    6104347 DRAGEN:CNLOH:chr1:6104348-6727324       N       <LOH>   1000    PASS
  END=6727324;REFLEN=622977;SVLEN=622977;LOHTYPE=AOH;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  1/1:2:0:1000:1000:1.9876:0.001988:0.993798:128.2:0.001:528:916:10,12:0.00766703

# Example GAIN call without minor-allele information
chr1    16605768        DRAGEN:GAIN:chr1:16605769-16645359      N       <DUP>   427     PASS
  END=16645359;REFLEN=39591;SVLEN=39591;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE
  ./1:6:.:1:.:6.27065:.:3.135326:404.457:.:23:0:6,11

# Example GAIN call with minor-allele information
chr1    16715826        DRAGEN:GAIN:chr1:16715827-16949283      N       <DUP>   744     PASS
  END=16949283;REFLEN=233457;SVLEN=233457;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  0/1:3:1:1000:99:3.08217:1.134239:1.541085:198.8:0.368:49:26:20,14:0.0384615

# Example GAIN LOH call
chr15   20212550        DRAGEN:GAINLOH:chr15:20212551-20421468  N       <LOH>   390     PASS
  END=20421468;REFLEN=208918;SVLEN=208918;LOHTYPE=AOH;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  1/1:6:0:1:1:5.90559:0.000000:2.952793:380.91:0:76:1:9,8:0

# Example MOSAIC GAIN call
chr2    89673674        DRAGEN:GAIN:chr2:89673675-89851643      N       <DUP>   1000    PASS
  END=89851643;REFLEN=177969;MOSAIC;SVLEN=177969;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE
  ./1:4:.:0:.:4.32403:.:2.162016:278.9:.:70:0:13,2

# Example LOSS call
chr1    25274774        DRAGEN:LOSS:chr1:25274775-25331683      N       <DEL>   226     PASS
  END=25331683;REFLEN=56909;SVLEN=56909;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  0/1:1:0:1000:1000:1.01085:0.000000:0.505426:65.2:0:7:10:5,1:0

# Example MOSAIC LOSS call
chrX    90207750        DRAGEN:LOSS:chrX:90207751-90458297      N       <DEL>   82      PASS
  END=90458297;REFLEN=250547;MOSAIC;SVLEN=250547;SVTYPE=CNV
  GT:CN:MCN:CNQ:MCNQ:CNF:MCNF:SM:SD:MAF:BC:AS:PE:OBF
  0/1:1:0:0:0:1.6186:0.459684:0.809302:104.4:0.284:10:27:3,11:0