Somatic CNV Calling Options

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--tumor-bam-input or --tumor-cram-input

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--cnv-normal-b-allele-vcf or --cnv-population-b-allele-vcf

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--sample-sex

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--cnv-normal-cnv-vcf

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--cnv-use-somatic-vc-vaf

To trigger the somatic CNV caller, the input alignments must use the tumor equivalent options, such as --tumor-bam-input or --tumor-cram-input. Support for running from FASTQ input (--tumor-fastq1, --tumor-fastq2, and --tumor-fastq-list) is not available in the somatic CNV caller. In addition, the somatic CNV caller does not support running directly from the mapper/aligner.

Use the --cnv-normal-b-allele-vcf option to specify a matched normal SNV VCF or --cnv-population-b-allele-vcf to specify a population SNP catalog. For more information on specifying b-allele loci, see Specify B-Allele Loci

If the sample sex is known, use the --sample-sex option to specify the sex. If it is not specified, the caller attempts to estimate the sample sex from the tumor alignments.

Use --cnv-normal-cnv-vcf to specify germline CNVs from a matched normal sample.

Use --cnv-use-somatic-vc-vaf to control whether the variant allele frequencies (VAFs) or somatic SNVs are used to help select the tumor model for the sample. For more information, see VAF Aware Mode

The following is an example command line for running the minimalsomatic CNV caller.

dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-map-align false \
--enable-cnv true \
--tumor-bam-input <TUMOR_BAM> \
--cnv-normal-b-allele-vcf <SNV_NORMAL_VCF> \
--sample-sex <SEX>

You can enable additional features when a matched-normal sample is also available. If a matched-normal sample is available, enable germline-aware mode and VAF-aware mode using the following example command-line. For more information on germline-aware mode and VAF-aware mode, see Germline-aware Mode and VAF Aware Mode.

 

dragen \

-r <HASHTABLE> \

--output-directory <OUTPUT> \

--output-file-prefix <SAMPLE> \

--enable-map-align false \

--enable-cnv true \

--tumor-bam-input <TUMOR_BAM> \

--cnv-normal-b-allele-vcf <SNV_NORMAL_VCF> \

--enable-vc true \

--bam-input <NORMAL_BAM>

--cnv-normal-cnv-vcf <CNV_NORMAL_VCF> \

--sample-sex <SEX>

If you provide an unmatched normal in place of a matched normal, you need to disable CNV calling or run in tumor-only mode. You can force tumor-only mode by omitting --cnv-normal-cnv-vcf, specifying --cnv-population-b-allele-vcf instead of --cnv-normal-b-allele-vcf, and adding --cnv-use-somatic-vc-vaf=false.