seqCNA: A Package for Copy Number Analysis of High-Throughput Sequencing Cancer DNA

This document guides the reader through the use of the seqCNA package. The aim of the package is to process high-throughput sequencing copy number data coming from tumoural samples, departing from SAM or BAM aligned reads up to the final stage of calling the copy numbers. It includes, among other features, an integrated summarization method, several filters based on a range of genomic and read-based characteristics and a normalization approach developed specifically for tumoural data. Overall, the package was conceived to be user-friendly, provide visual assessment at each step and keep a simple and limited parameterization.