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SCHISM specifications


Unique identifier OMICS_16121
Alternative name SubClonal Hierarchy Inference from Somatic Mutations
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A tab-delimited table listing somatic mutation allele specific read counts and integer copy number value, or a tab-delimited list of the estimated value and standard error of cellularity for each somatic mutation in each tumor sample, a tab-delimited file that assigns each somatic mutation to a mutation cluster.
Output data The subclone tree reconstruction.
Operating system Unix/Linux
License Other
Computer skills Advanced
Version 1.1.2
Stability Stable
Matplotlib, igraph c core, python-igraph, numpy, scipy, PyYAML, sklearn
Source code URL
Maintained Yes




No version available


  • person_outline Rachel Karchin

Publication for SubClonal Hierarchy Inference from Somatic Mutations

SCHISM citations


High grade serous ovarian carcinomas originate in the fallopian tube

Nat Commun
PMCID: 5653668
PMID: 29061967
DOI: 10.1038/s41467-017-00962-1

[…] The tumor subclonality phylogenetic reconstruction algorithm SCHISM was used to infer tumor subclonal hierarchies from the set of confidently called somatic mutations in each patient. Given the estimates of genome-wide copy number profile, most copy number aber […]


Advances in understanding tumour evolution through single cell sequencing*

Biochim Biophys Acta
PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] prevalences of both SNV and CNA data . However it relies on other tools to accurately estimate these prevalences in a preprocessing step and is restricted to two samples such as tumour/relapse pairs. SCHISM  also relies on pre-established cellular prevalences. The inference is then a two-step process: It first uses a hypothesis testing framework to establish subclones and their pairwise relationsh […]


The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community Based Rapid Autopsy Program “CASCADE”

PLoS Med
PMCID: 5189956
PMID: 28027312
DOI: 10.1371/journal.pmed.1002204

[…] ted to 0.1. All other genotype prior weights were left as 1. From the PyClone output, the median clonality for each mutation (or cancer cell fraction) was clustered via affinity propagation using the Schism package []. Mutation clusters were reviewed to separate agglomerated private subclones if needed, and then the reviewed clusters were supplied to Schism’s genetic algorithm to construct a multi […]


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SCHISM funding source(s)
This work was supported by funds from National Cancer Institute R01CA179991.

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