Copy Number Variant Detection (WGS) outputs
The Copy Number Variant Detection (WGS) tool produces the following outputs:
- CNVs from WGS A track containing all detected CNVs with the CNV region and the following information:
- Length The length of the CNV in base pairs.
- Median read counts per window The median read count per window that is part of the CNV.
- Consequence The consequence of the detected CNV, i.e. "Gain" or "Loss".
- Copy number The predicted copy number of the CNV.
- Score A score reflecting the amount of evidence of the CNV being a true event.
- Average mappability score The average Umap mappability score of the CNV. This annotation is only present if a Umap mappability track was provided when running the tool.
- Distance to centromere The distance to the nearest centromere.
- N-masked and low mappability regions A track containing N-masked regions and, if a Umap mappability track was provided, regions with low mappability. It outlines the masked regions and the following information:
- Type Specification of the type of masking.
- Average mappability score The average Umap mappability score of the masked region.
- CNV WGS report A detailed report about the detected CNVs. It contains the following sections:
- Summary A summary table containing general information about the sample, the window size and the identified CNVs.
- References A table listing each of the analyzed chromosomes together with the number of reads mapped to the chromosome and the average coverage.
- CNVs per chromosome A table listing each of the analyzed chromosomes together with the number of losses and gains and the number of positions affected by gains and losses.
- Visualization of CNVs An overview plot depicting identified CNVs on all the chromosomes in the genome.
- Chromosome window read count distributions Plot of the normalized mean read count per window versus the standard deviation for the read count per window. Each chromosome is represented by one dot. The selected cluster is black, and chromosomes that are not part of the cluster are grey. A red dot is positioned at the center of the selected cluster. The mean coverage at the center of the selected cluster is defined as the expected coverage for a diploid region.
- Size distribution A table summarizing the sizes of identified CNVs.
- Coverage per window and identified CNVs A section containing a plot for all chromosomes combined and one for each chromosome. The plots show normalized read counts per window versus the genomic position. Identified CNVs and masked regions are also illustrated. The plots contain one dot for each window, but dots may be collapsed if they cannot be visually discerned. Per default, the Y-axis is scaled to fit 95% of all dots; however, identified CNVs will always be included and this can result in more than 95% of all dots being visible in the plot.