SV VCF Quality

Owned by Sara Haers
Apr 29, 2022
1 min read

The SV Quality page shows some general statistics on the uploaded SV/CNV file, if uploaded in VCF format. It is available through the drop-down menu next to the sample name on top of the screen.

At the top right of the screen, Moon indicates the genome build of the file (GRCh37 or GRCh38) that was extracted from the SNV VCF of the sample. Uploaded SV/CNV files should be called against the same genome build as the SNV VCF file, and this is assumed as such for annotation.

Below, in the SV quality tab, some statistics are shown:

  • Total number of called SV/CNV variants in the VCF

  • Percentage of SV types (deletions, duplications, insertions, inversions, BNDs) in the VCF

  • Distribution of SV size by SV type

Determination of the quality parameters is only based on calls with a “PASS” or empty indication (“.”) in the VCF’s Filter field. Calls with other information in the VCF’s Filter field are not considered by Moon for annotation and analysis.

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.