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.

Download and Installation

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 Contributors
External Contributors


  • High-definition reconstruction of clonal composition in cancer.

    Fischer A, Vázquez-García I, Illingworth CJR and Mustonen V

    Cell reports 2014;7;5;1740-1752