Multisample CNV Calling

Multisample CNV calling is possible starting from tangent normalized counts files (*.tn.tsv.gz) specified with the --cnv-input option (one per sample). Multisample CNV analysis benefits from using joint segmentation to increase the sensitivity of detection of copy number variable segments. For each copy number variable segment identified, the copy number genotype of each sample is emitted in a single VCF entry to facilitate annotation and interpretation.

dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-cnv true \
--cnv-input <FATHER_TN_TSV> \
--cnv-input <MOTHER_TN_TSV> \
--cnv-input <PROBAND_TN_TSV> \
--pedigree-file <PEDIGREE_FILE>

De Novo CNV Calling Options

Make sure all input samples have gone through the same single sample workflow and have identical intervals. If the samples are WES inputs, then you must generate the samples using the same panel of normals, and the autosomal intervals for all samples must match.

The following options are used in DeNovo CNV calling:

Option	Description
--cnv-input	For DeNovo CNV calling, this specifies the input tangent-normalized signal files (*.tn.tsv) from the single sample runs. This option can be specified multiple times, once for each input sample.
--cnv-input	For DeNovo CNV calling, this specifies the input tangent-normalized signal files (*.tn.tsv) from the single sample runs. This option can be specified multiple times, once for each input sample.
--cnv-filter-de-novo-qual	Phred-scaled threshold at which a putative event in the proband sample is marked as DeNovo. Default value is 0.125.
--pedigree-file	Pedigree file specifying the relationship between the input samples.