Quality
The Quality page shows some general statistics on the imported VCF (only for SNVs). 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 VCF. If no information on genome build is available in the VCF header, GRCh37 is assumed.
Below, some quality parameters are shown. For some of the provided parameters, Moon indicates whether the value is within the expected range or not (green: expected range, red: deviating from the expected value). Hovering over each icon gives you some more information on the expected range.
The following parameters are provided:
Total number of called variants in the VCF with the indication of the number of SNVs and indels
Heterozygous/homozygous ratio
Transition/transversion ratio
% variants with allelic imbalance
Average depth of coverage
Median depth of coverage
Maximum depth
Depth distribution diagram
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 VCF files might lead to false positive and false negative interpretation results. It is recommended to assess the overall quality of the input VCF prior to variant interpretation.