SV/CNV VCF

Owned by Sara Haers
Apr 29, 2022
2 min read

Import SV/CNVs

A file containing structural variant calls (SV) and copy number variation (CNV) can be optionally added to an existing sample on the Patient Info screen. These variants can be provided either in VCF format (according to the specifications defined at https://samtools.github.io/hts-specs/VCFv4.3.pdf) or as output from Nexus Copy number. Files can be either uncompressed or uploaded as a .gzip file.

The following fields are required in SV/CNV VCF files in order to allow a Moon analysis:

  • Chromosome

  • Position

  • END (defined in INFO field)

  • SVTYPE (defined in INFO field). Supported SV types are DEL, DUP, INS, INV, BND.

  • GT (genotype)

If copy number is provided in the VCF (CN), this info will be taken into account. If this is not available, CN will be annotated based on the genotype information and SVTYPE.

If any of the above required fields are missing from the SV/CNV VCF no analysis can be performed by Moon (for both SNVs and SV/CNVs).

 

For Nexus Copy number files, the following information should be included in the uploaded file:

  • Chromosome Region (genomic coordinates of the event)

  • Event (CN Gain / CN Loss / Homozygous Copy Loss)

 

To add an SV file to an existing sample, either a proband or a healthy family member, follow the steps below:

  • On the Samples screen, click the Patient info icon next to the sample name of interest.

  • Drag and drop the file corresponding to the sample of interest in the upload area at the bottom of the screen.

  • Once the SV file is uploaded. Moon displays the SV VCF file name. You have the option to remove the SV file by clicking Remove it.

Uploaded SV/CNV files should be called against the same genome build as the SNV VCF file. This is assumed as such for annotation.

Low quality input files might lead to false positive and false negative interpretation results. It is recommended to assess the overall quality of the input prior to variant interpretation.