Copy number information can be obtained from off-target reads. (A) Screenshot from the IGV genome browser, showing an example of a genomic region with sequence reads mapping to the genome before and after removal of reads in Model-based Analysis for ChIPseq (MACS) called peaks. In addition, the location of MACS-peaks, capture regions, and genes are shown. (B) Germline DNA sample C41 was subjected to WES with capture set Agilent SureSelect Human Exon Kit V4. The nature of MACS-peaks that do not overlap capture regions is displayed. The fraction of these orphan peaks that overlap with pseudogene or Ensembl exons, that do not map to any of the reference genome chromosomes, that are unmappable, and that do not belong to any of these categories are shown. (C) The distribution of sequence reads of both germline and tumor DNA samples is shown for the indicated capture sets. Sequence reads are classified into one of these categories: (1) low mapping quality reads (Phred-score < 37 and/or reads do not pair properly); (2) mitochondrial reads; (3) reads in MACS-peaks; (4) remaining reads. Error bars represent standard deviations. (D) Germline DNA sample C45 was subjected to WES, and the amount of reads after compensation for reduced effective bin size is calculated and compared to the corresponding read counts from an exon-based method. Density plots of the number of sequence reads per data point are shown for each method. (E) A flowchart of the steps incorporated in the CopywriteR tool.