MiniCN

Copy Number Alteration Caller for Small Targeted Panels

MiniCN is a lightweight pipeline for DNA copy number calling on small, amplicon-based targeted sequencing panels (< 1 Mb) using GATK-like coverage files. It supports either matched tumor–normal pairs or a pool-of-normals (PON) for coverage normalization.

MiniCN was originally created for a gene panel (~60 kb) with amplicons covering the full coding regions of ~20 genes, and introns for only a subset of the genes.

Installation

The easiest way to install the R package miniCN is via the devtools package:

install.packages("devtools")
library(devtools)
devtools::install_github("SveenLab/MiniCN")
library(miniCN)

This package was constructed under R version 4.3.2 (2023-10-31).

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Quick Start

library(miniCN)

# Example inputs bundled with the package
sample_csv <- system.file("extdata", "sample_sheet.csv", package = "MiniCN")
panel_file <- system.file("extdata", "panel_genes.txt", package = "MiniCN")

# Output directory
out <- "outputs"
if (!dir.exists(out)) {
  dir.create(out, showWarnings = FALSE, recursive = TRUE)
}

# Run copy-number calling
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
  run_caller(sample_csv = sample_csv, outdir = out, panel_path = panel_file)
}

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Output files (in outdir):

• 0_Excluded_Targets.tsv
• 1_Amplicons_CN.tsv
• 2_Samples_QC.tsv
• 3_Gene_CN_Final.tsv
• <sample>_CN_plots.pdf

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Input formats:

Coverage files

These input files are derived from results of the GATK DepthOfCoverage tool. All coverage files names should have suffix _coverage.sample_interval_summary . They should be tab-delimited text files with a header and contain the following columns (case-sensitive):

Column	Description
target (or interval_id, interval)	format chr:start-end
total_coverage (or totalcount, totalcounts, count, counts, coverage, totalcoverage)	total read coverage

Example GATK’s DepthOfCoverage command:

gatk DepthOfCoverage \
  -R reference.fasta \
  -O sample_coverage \
  -L targets.interval_list \
  -I sample.bam

The output file sample_coverage.sample_interval_summary can be directly used as MiniCN input.

Sample sheet (.csv)

Column	Description
Tumor Folder	folder path with tumor coverage files
Tumor File	tumor coverage file name
Normal Folder	folder path with Normal coverage files
Normal File	Normal coverage file name

Example:

Tumor Folder,Tumor File Name,Normal Folder,Normal File Name
examples/,tumorA,examples/,normalA

Using a PON: set Normal File Name to PON_median and point Normal Folder to a directory containing more than 2 files.

Example:

Tumor Folder,Tumor File Name,Normal Folder,Normal File Name
examples/,tumorA,examples/PON_normals/,PON_median

Panel genes

Plain text, one HGNC symbol per line (e.g., EGFR).

Symbols are validated via org.Hs.eg.db .

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Key Parameters

Flag	Description	Default
pc	pseudocount	0.5
HIGH_AMP_T	high-amplification copy number threshold	log2(17/2) or ~3.09
LOW_AMP_T	low-amplification copy number threshold	log2(7/2) or ~1.81
GAIN_T	gain copy number threshold	log2(3/2) or ~0.58
LOSS_T	loss copy number threshold	log2(1/2) or -1.0
DEEP_DEL_T	deletion copy number threshold	-2.0
MIN_AMPLICONS	minimum number of amplicons supporting respective changes	2.0
MIN_GENE_Z	minimum z-score cutoff for gains and losses	3.0
MAX_Q_VALUE	maximum q-value cutoff for gains and losses	0.05

Citation

To cite package ‘MiniCN’ in publications use:

Nunes, L. (2025). MiniCN: Copy Number Alteration Caller for Small Targeted Panels. R package version 0.1.0. SveenLab, Dept. Molecular Oncology, ICR, Oslo University Hospital. URL: https://github.com/SveenLab/miniCN.