High-definition reconstruction of clonal composition

cloneHD is a software for reconstructing the subclonal structure of a population from short-read sequencing data. Read depth data, B-allele count data and somatic nucleotide variant (SNV) data can be used for the inference. cloneHD can estimate the number of subclonal populations, their fractions in the sample, their individual total copy number profiles, their B-allele status and all the SNV genotypes with high resolution.

filterHD is a general purpose probabilistic filtering algorithm for one-dimensional discrete data, similar in spirit to a Kalman filter. It is a continuous state space Hidden Markov model with Poisson or Binomial emissions and a jump-diffusion propagator. It can be used for scale-free smoothing, fuzzy data segmentation and data filtering.


The current stable release, as well as pre-compiled executable binaries for Mac OS X and GNU Linux (64bit), can be found on the Github repository.

Sanger Institute Contributors

Previous contributors

Photo of Dr Ville Mustonen

Dr Ville Mustonen

Former CDF Group Leader

External Contributors

Photo of Andrej Fischer

Andrej Fischer