Detection of CNVs between 2-10kb¶
Detection of CNVs between 2 and 10 kb was introduced to the Rare Disease pipeline on July 28th 2021 (NGIS Danny release). All analysis performed after this date includes this pipeline enhancement. For any given referral, the limitations described in the Summary of Findings will indicate if small CNV analysis was performed (see Pipeline limitations for further details).
Note
Detection of CNVs between 2 and 10kb in size is performed for probands only.
CNVs between 2 and 10 kb are identified using a combination of two different variant callers that utilise different signals to detect copy number variation, DRAGEN CNV and DRAGEN SV, which use read depth and anomalously mapped/split reads respectively.
CNVs <10 kb detected by DRAGEN CNV that are also supported by CNVs detected by DRAGEN SV with a minimum reciprocal overlap of at least 50% and with matching CNV type (deletion or duplication) are considered to be high quality CNVs and are subsequently included for annotation and reporting. For high quality CNVs, the filter status in the VCF file for the proband is set to PASS, and additional annotation is added to the VCF file including the CNV coordinates detected by DRAGEN SV (which are likely more accurate due to the use of split reads in CNV detection) and a flag to indicate a CNV is de novo where parental data are available.
The updated version of the CNV VCF file for the proband is renamed to “
| Field | Description |
|---|---|
MANTA_SUPPORT |
(Flag) CNV supported by DRAGEN SV (reciprocal overlap >= 50%) |
MANTA_POS |
Coordinates of the overlapping DRAGEN SV call |
DN |
(Flag) De novo variant, based on DRAGEN SV joint calling |
DN_TYPE |
Type of de novo variant, based on DRAGEN SV joint calling (format: probandGT-fatherGT-motherGT) |
PREV_FILTER |
Original non-PASS filter in DRAGEN CNV VCF file before small CNV enhancement |
Note
MANTA_SUPPORT and MANTA_POS flags are legacy names prior to the conversion of MANTA to DRAGEN SV