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PyCloneQC

Quality checker for PyClone. Work in progress. This tool supplants the PyClone analysis and requires PyClone version 0.13. For more information about PyClone, see https://bitbucket.org/aroth85/pyclone/wiki/Home and Roth et al., Nat Methods 11: 396, 2014.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Antti Hakkinen (antti.e.hakkinen@helsinki.fi)
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Requires Python ; PyClone
Source files component.xml launcher.py
Usage Example with default values

Inputs

Name Type Mandatory Description
config YAML Mandatory PyClone configuration file
trace BinaryFolder Optional PyClone trace directory (overrides that specified in the configuration file)
mutationFiles Array<YAML> Optional Mutation files in the YAML format

Outputs

Name Type Description
corr CSV Results of the correlation analysis of the traces
conv CSV Results of the convergence analysis of the traces
plots BinaryFolder Output directory for the plots

Parameters

Name Type Default Description
infCoverage float 1e100 Variants with coverage no smaller than the specified will be considered as known, and will flaggedrto be excluded from the analysis.
plotType string "" Comma separated list of the requested plot types. Options: "corr", "conv".
tolerance float 0.05 Relative level of changes at which the correlations are assumed to be vanished and the series converged

Test cases

Test case Parameters IN
config
IN
trace
IN
mutationFiles
OUT
corr
OUT
conv
OUT
plots
default (missing) config trace (missing) corr conv (missing)

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