GenCHORD is a tool for inferring the average copy-number of large contiguous blocks of sequences within a genome from the raw coverage data, using Bayesian methods to infer the underlying stochastic parameters and hence extract a moving average, which is constrained to integer multiples of a fundamental frequency.
This tool was designed for analysing Chromothripsis in conjunction with the steppingStone tool, but has applications outside of that usecase.
The tool has been verified to work on data from both long and short read platforms.