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.

Multisample CNV calling is recommended for only WGS analysis.

The following is an example command line for running a trio analysis:

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

All input samples should have gone through the same single sample WGS workflow and must have identical intervals.

The following options are used in DeNovo CNV calling:

•

--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 0.10.

•

--pedigree-file—Pedigree file specifying the relationship between the input samples.