A target gene will be called a gain/loss if the log ratio of depth is this number of standard deviations above/below the mean of the copy number controls

refFlat file for reference genome

Bed file of all genes. Columns: chrom, start, stop, gene name, value (arbitrary), strand (+/-)

Reference genome fasta.

hg19 or hg38. Other genomes not supported

Array of bam files. Contains cfDNA/plasma samples. Should have .bai files in same directory

Tab delimited bed file describing genes included in the targeted panel, including controls. Columns should contain: chromosome, start position, end position, gene name, description (can be anything, unless it is a control gene, in which case it should be labeled CN-control)

Bed file of probes used to target desired target regions. Can be supplied as file path or File

Array of bam files. Should be in the same order as sample_bams (ie the nth sample in each array are matched).

Array of bams used as unmatched, panel of normals. Should have .bai files in same directory